REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.DESMYTER,T.R.TRANSUE,M.A.GHAHROUDI,M.H.THI, REMARK 1 AUTH 2 F.POORTMANS,R.HMAERS,S.MUYLDERMANS,L.WYNS REMARK 1 TITL CRYSTAL STRUCTURE OF A CAMEL SINGLE-DOMAIN VH REMARK 1 TITL 2 ANTIBODY FRAGMENT IN COMPLEX WITH LYSOZYME REMARK 1 REF NAT.STRUCT.BIOL. V. 9 803 1998 REMARK 1 REFN ISSN 1072-8368 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 25796 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 + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1298 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7544 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.26 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.453 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.324 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.007 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.026 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.021 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.094 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.183 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.235 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : 0.183 ; 0.300 REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : 0.000 ; 15.000 REMARK 3 PLANAR (DEGREES) : 3.200 ; 7.000 REMARK 3 STAGGERED (DEGREES) : 25.900; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 25.800; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.833 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.524 ; 3.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 0.810 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 1.390 ; 3.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: CHAINS A, B, C AND D ARE RNASE A REMARK 3 MOLECULES CHAINS K, L, M AND N ARE ANTIBODY MOLECULES SEPARATE REMARK 3 NCS WAS APPLIED TO EACH GROUP OF MOLECULES REMARK 4 REMARK 4 1BZQ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-NOV-98. REMARK 100 THE RCSB ID CODE IS RCSB000024. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 293.0 REMARK 200 PH : 6.4 REMARK 200 NUMBER OF CRYSTALS USED : 2 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : SI CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25413 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11100 REMARK 200 FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.33600 REMARK 200 FOR SHELL : 3.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1RUV AND PDB ENTRY 1MEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HANGING DROP METHOD. 5 MG/ML OF THE REMARK 280 COMPLEX RESERVOIR SOLUTION IS 0.1 M POTASSIUM PHOSPHATE PH 6.4 REMARK 280 15 TO 20% W/V PEG 8000, VAPOR DIFFUSION - HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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: A, L 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, N 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, M 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 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, K 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 39 CA - CB - CG ANGL. DEV. = 14.5 DEGREES REMARK 500 ASP B 283 CB - CA - C ANGL. DEV. = 12.4 DEGREES REMARK 500 ARG C 433 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 CYS C 440 CA - CB - SG ANGL. DEV. = 7.4 DEGREES REMARK 500 ARG K 838 NE - CZ - NH2 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG K 872 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 ARG K 872 NE - CZ - NH2 ANGL. DEV. = -5.3 DEGREES REMARK 500 ARG K 904 CD - NE - CZ ANGL. DEV. = 14.1 DEGREES REMARK 500 ARG K 904 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG L1122 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG M1219 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES REMARK 500 ASP M1252 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES REMARK 500 THR M1318 N - CA - CB ANGL. DEV. = 12.6 DEGREES REMARK 500 ARG N1445 CD - NE - CZ ANGL. DEV. = 11.6 DEGREES REMARK 500 ARG N1472 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG N1472 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG N1524 CD - NE - CZ ANGL. DEV. = 10.7 DEGREES 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 SER A 16 27.62 -71.11 REMARK 500 ALA A 19 148.66 -174.74 REMARK 500 SER A 21 -82.37 -54.55 REMARK 500 SER A 22 -157.70 -79.03 REMARK 500 HIS A 48 53.08 -102.32 REMARK 500 GLN A 60 -135.89 -102.19 REMARK 500 ASN A 71 36.13 -95.99 REMARK 500 THR A 87 -167.68 -71.17 REMARK 500 SER B 216 26.79 -72.83 REMARK 500 ALA B 219 145.74 179.22 REMARK 500 SER B 221 -79.40 -57.60 REMARK 500 SER B 222 -160.57 -75.93 REMARK 500 HIS B 248 50.82 -99.87 REMARK 500 GLN B 260 -135.96 -102.66 REMARK 500 ASN B 271 33.86 -97.42 REMARK 500 THR B 287 -166.84 -70.16 REMARK 500 ASP B 321 -63.70 -90.95 REMARK 500 SER C 416 25.82 -69.28 REMARK 500 ALA C 419 148.79 -178.13 REMARK 500 SER C 421 -82.46 -54.51 REMARK 500 SER C 422 -158.46 -77.90 REMARK 500 HIS C 448 50.55 -101.89 REMARK 500 GLN C 460 -138.62 -105.26 REMARK 500 ASN C 471 34.20 -96.99 REMARK 500 THR C 487 -169.58 -68.81 REMARK 500 SER D 616 33.92 -74.39 REMARK 500 ALA D 619 148.07 -179.02 REMARK 500 SER D 621 -81.39 -54.52 REMARK 500 SER D 622 -159.67 -74.83 REMARK 500 ASN D 634 31.22 72.25 REMARK 500 HIS D 648 55.69 -104.28 REMARK 500 GLN D 660 -137.01 -104.00 REMARK 500 ASN D 671 35.32 -98.50 REMARK 500 THR D 687 -167.55 -67.74 REMARK 500 ASP D 721 -62.97 -92.35 REMARK 500 TYR K 829 -168.38 -116.38 REMARK 500 LYS K 843 179.20 -52.68 REMARK 500 GLU K 902 -122.91 47.96 REMARK 500 SER K 921 157.40 -49.75 REMARK 500 TYR L1029 -168.15 -112.36 REMARK 500 LYS L1043 179.66 -59.14 REMARK 500 ALA L1092 171.91 179.94 REMARK 500 GLU L1102 -122.98 44.99 REMARK 500 SER L1121 156.74 -48.45 REMARK 500 TYR M1229 -166.69 -115.07 REMARK 500 LYS M1243 -177.38 -51.64 REMARK 500 ASN M1277 59.03 -91.68 REMARK 500 GLU M1302 -123.61 48.90 REMARK 500 TYR N1429 -164.94 -114.66 REMARK 500 LYS N1443 -176.27 -48.98 REMARK 500 ASN N1477 58.06 -90.82 REMARK 500 GLU N1502 -123.20 49.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 2001 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 2002 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 C 2003 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 D 2004