REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.TAKAHASHI,H.TAMURA,N.SHIMBA,I.SHIMADA,Y.ARATA REMARK 1 TITL ROLE OF THE DOMAIN-DOMAIN INTERACTION IN THE REMARK 1 TITL 2 CONSTRUCTION OF THE ANTIGEN COMBINING SITE. A REMARK 1 TITL 3 COMPARATIVE STUDY BY 1H-15N SHIFT CORRELATION NMR REMARK 1 TITL 4 SPECTROSCOPY OF THE FV AND FAB FRAGMENT OF REMARK 1 TITL 5 ANTI-DANSYL MOUSE MONOCLONAL ANTIBODY REMARK 1 REF J.MOL.BIOL. V. 243 494 1994 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH H.TAKAHASHI,E.SUZUKI,Y.ISHIMADAARATA REMARK 1 TITL DYNAMICAL STRUCTURE OF THE ANTIBODY COMBINING SITE REMARK 1 TITL 2 AS STUDIED BY 1H-15N SHIFT CORRELATION NMR REMARK 1 TITL 3 SPECTROSCOPY REMARK 1 REF BIOCHEMISTRY V. 31 2464 1992 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 3 REMARK 1 AUTH A.ODAKA,J.I.KIM,H.TAKAHASHI,I.SHIMADA,Y.ARATA REMARK 1 TITL ISOTOPE-EDITED NUCLEAR MAGNETIC RESONANCE STUDY OF REMARK 1 TITL 2 FV FRAGMENT OF AN ANTI- DANSYL MOUSE MONOCLONAL REMARK 1 TITL 3 ANTIBODY: RECOGNITION OF THE DANSYL HAPTEN REMARK 1 REF BIOCHEMISTRY V. 31 10686 1992 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 4 REMARK 1 AUTH H.TAKAHASHI,T.IGARASHI,I.SHIMADA,Y.ARATA REMARK 1 TITL PREPARATION OF THE FV FRAGMENT FROM A SHORT-CHAIN REMARK 1 TITL 2 MOUSE IGG2A ANTI-DANSYL MONOCLONAL ANTIBODY AND REMARK 1 TITL 3 USE OF SELECTIVELY DEUTERATED FV ANALOGUES FOR REMARK 1 TITL 4 TWO- DIMENSIONAL 1H NMR ANALYSES OF REMARK 1 TITL 5 ANTIGEN-ANTIBODY INTERACTIONS REMARK 1 REF BIOCHEMISTRY V. 30 2840 1991 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 5 REMARK 1 AUTH H.TAKAHASHI,A.ODAKA,S.KAWAMINAMI,C.MATSUNAGA, REMARK 1 AUTH 2 K.KATO,I.SHIMADA,Y.ARATA REMARK 1 TITL MULTINUCLEAR NMR STUDY OF THE STRUCTURE OF THE FV REMARK 1 TITL 2 FRAGMENT OF ANTI-DANSYL MOUSE IGG2A ANTIBODY REMARK 1 REF BIOCHEMISTRY V. 30 6611 1991 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 6 REMARK 1 AUTH T.KIMNAKANO,T.HIGUCHI,M.HIROBE,I.SHIMADA,Y.ARATA REMARK 1 TITL CONFORMATION AND STEREOSELECTIVE REDUCTION OF REMARK 1 TITL 2 HAPTEN SIDE CHAIN IN THE ANTIBODY COMBINING SITE REMARK 1 REF J.AM.CHEM.SOC. V. 113 9392 1991 REMARK 1 REFN ISSN 0002-7863 REMARK 1 REFERENCE 7 REMARK 1 AUTH T.IGARASHI,M.SATO,Y.KATSUBE,K.TAKIO,T.TANAKA, REMARK 1 AUTH 2 M.NAKANISHI,Y.ARATA REMARK 1 TITL STRUCTURE OF A MOUSE IMMUNOGLOBULIN G THAT LACKS REMARK 1 TITL 2 THE ENTIRE CH1 DOMAIN: PROTEIN SEQUENCING AND REMARK 1 TITL 3 SMALL-ANGLE X-RAY SCATTERING STUDIES REMARK 1 REF BIOCHEMISTRY V. 29 5725 1990 REMARK 1 REFN ISSN 0006-2960 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 1.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 32150 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3216 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 26 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.57 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 780 REMARK 3 BIN R VALUE (WORKING SET) : 0.3400 REMARK 3 BIN FREE R VALUE : 0.3300 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 11.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 83 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.037 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1872 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 400 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.17 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.02 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 27.39 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.58 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : GAUSS REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ALL ATOMS IN THE ASYMMETRIC UNIT REMARK 3 WERE REFINED REMARK 4 REMARK 4 2DLF COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-AUG-99. REMARK 100 THE RCSB ID CODE IS RCSB007339. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUL-98 REMARK 200 TEMPERATURE (KELVIN) : 112 REMARK 200 PH : 6.75 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU ULTRAX 18 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : DOUBLE FOCUSING MIRROR (PT REMARK 200 COATED AND NI COATED) REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32405 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 11.100 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 42.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.52 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 0.31800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: 1IGF REMARK 200 REMARK 200 REMARK: DATA WERE COLLECTED BY OSCILLATION METHOD REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALLIZATION CONDITIONS: REMARK 280 TEMPERATURE AT 20C. PRECIPITANT SOLUTION CONTAINED 1 AMMONIUM REMARK 280 SULFATE AND 0.025 M SODIUM CACODYLATE (PH 6.75). 5 MG/ML OF FV REMARK 280 FRAGMENT., VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 28.64500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 26.81500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.46500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 26.81500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.64500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.46500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 400 REMARK 400 COMPOUND REMARK 400 COMPAOUND REMARK 400 THE FV FRAGMENT WAS PROPARED BY A PROTEOLYTIC DIGESTION OF REMARK 400 ANTI-DANSYL MONOCLONAL ANTIBODY. THE FV FRAGMENT WAS COMPOSE REMARK 400 OF 237 AMINO ACID RESIDUES (113 RESIDUES IN THE VL DOMAIN AN REMARK 400 124 RESIDUES IN THE VH DOMAIN). REMARK 400 REMARK 400 THE FV FRAGMENT WAS PREPARED BY A PROTEOLYTIC DIGESTION OF REMARK 400 ANTI-DANSYL MONOCLONAL ANTIBODY. THE FV FRAGMENT IS REMARK 400 COMPOSED OF 237 AMINO ACID RESIDUES (113 RESIDUES IN THE REMARK 400 VL DOMAIN AND 124 RESIDUES IN THE VH DOMAIN). REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ALA H 113 REMARK 465 GLU H 114 REMARK 465 PRO H 115 REMARK 465 ARG H 116 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OG SER L 56 O HOH L 568 1.95 REMARK 500 OG SER L 100 O HOH L 535 2.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LEU L 47 -60.77 -109.88 REMARK 500 VAL L 51 -51.68 73.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG L 54 0.09 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH L 552 DISTANCE = 5.51 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: H-1 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: NULL REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 L 401 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 H 402