HEADER IMMUNE SYSTEM 23-JAN-09 2W9D TITLE STRUCTURE OF FAB FRAGMENT OF THE ICSM 18 - ANTI-PRP THERAPEUTIC TITLE 2 ANTIBODY AT 1.57 A RESOLUTION. COMPND MOL_ID: 1; COMPND 2 MOLECULE: ICSM 18-ANTI-PRP THERAPEUTIC FAB HEAVY CHAIN; COMPND 3 CHAIN: H; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: ICSM 18-ANTI-PRP THERAPEUTIC FAB LIGHT CHAIN; COMPND 6 CHAIN: L SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_TAXID: 10090; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 6 ORGANISM_TAXID: 10090 KEYWDS IMMUNE SYSTEM, PRION, PRP, FAB EXPDTA X-RAY DIFFRACTION AUTHOR S.V.ANTONYUK,C.R.TREVITT,R.W.STRANGE,G.S.JACKSON,D.SANGAR, AUTHOR 2 M.BATCHELOR,S.JONES,T.GEORGIOU,S.COOPER,C.FRASER,A.KHALILI-SHIRAZI, AUTHOR 3 A.R.CLARKE,S.S.HASNAIN,J.COLLINGE REVDAT 6 13-DEC-23 2W9D 1 REMARK LINK REVDAT 5 11-MAR-20 2W9D 1 REMARK SEQRES LINK REVDAT 4 13-JUL-11 2W9D 1 VERSN REVDAT 3 10-MAR-09 2W9D 1 JRNL REVDAT 2 24-FEB-09 2W9D 1 JRNL REVDAT 1 03-FEB-09 2W9D 0 JRNL AUTH S.V.ANTONYUK,C.R.TREVITT,R.W.STRANGE,G.S.JACKSON,D.SANGAR, JRNL AUTH 2 M.BATCHELOR,S.COOPER,C.FRASER,S.JONES,T.GEORGIOU, JRNL AUTH 3 A.KHALILI-SHIRAZI,A.R.CLARKE,S.S.HASNAIN,J.COLLINGE JRNL TITL CRYSTAL STRUCTURE OF HUMAN PRION PROTEIN BOUND TO A JRNL TITL 2 THERAPEUTIC ANTIBODY. JRNL REF PROC.NATL.ACAD.SCI.USA V. 106 2554 2009 JRNL REFN ISSN 0027-8424 JRNL PMID 19204296 JRNL DOI 10.1073/PNAS.0809170106 REMARK 2 REMARK 2 RESOLUTION. 1.57 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.3.0037 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 3 NUMBER OF REFLECTIONS : 51289 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) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2725 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.57 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.61 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2513 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 63.49 REMARK 3 BIN R VALUE (WORKING SET) : 0.3030 REMARK 3 BIN FREE R VALUE SET COUNT : 116 REMARK 3 BIN FREE R VALUE : 0.3350 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3260 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 667 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.06000 REMARK 3 B22 (A**2) : 0.68000 REMARK 3 B33 (A**2) : -0.63000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.102 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.099 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.065 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.460 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3521 ; 0.006 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2326 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4856 ; 1.229 ; 1.949 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5755 ; 0.804 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 484 ; 6.597 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 133 ;37.350 ;24.436 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 574 ;11.624 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;11.124 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 552 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3966 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 690 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 578 ; 0.180 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2310 ; 0.188 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1654 ; 0.174 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1917 ; 0.082 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 464 ; 0.120 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 5 ; 0.223 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 18 ; 0.119 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 58 ; 0.204 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 54 ; 0.125 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2283 ; 0.518 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 886 ; 0.110 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3652 ; 0.838 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1459 ; 1.201 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1173 ; 1.652 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : H 1 H 114 REMARK 3 ORIGIN FOR THE GROUP (A): -4.6460 8.5490 51.0440 REMARK 3 T TENSOR REMARK 3 T11: -0.1398 T22: -0.1341 REMARK 3 T33: -0.1479 T12: -0.0159 REMARK 3 T13: -0.0118 T23: 0.0091 REMARK 3 L TENSOR REMARK 3 L11: 2.5562 L22: 0.8191 REMARK 3 L33: 1.3216 L12: 0.4430 REMARK 3 L13: 0.7336 L23: 0.5031 REMARK 3 S TENSOR REMARK 3 S11: 0.1238 S12: -0.1734 S13: -0.1801 REMARK 3 S21: 0.1575 S22: -0.0580 S23: -0.0072 REMARK 3 S31: 0.1386 S32: -0.0539 S33: -0.0658 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : H 115 H 215 REMARK 3 ORIGIN FOR THE GROUP (A): 3.6490 7.2020 20.8630 REMARK 3 T TENSOR REMARK 3 T11: -0.1644 T22: -0.1059 REMARK 3 T33: -0.1429 T12: -0.0002 REMARK 3 T13: 0.0069 T23: -0.0357 REMARK 3 L TENSOR REMARK 3 L11: 3.2470 L22: 1.3255 REMARK 3 L33: 1.0399 L12: 0.6277 REMARK 3 L13: -0.6696 L23: -0.2230 REMARK 3 S TENSOR REMARK 3 S11: -0.0475 S12: 0.2845 S13: 0.0814 REMARK 3 S21: -0.0981 S22: 0.0697 S23: -0.1203 REMARK 3 S31: 0.0079 S32: 0.0069 S33: -0.0221 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : L 1 L 106 REMARK 3 ORIGIN FOR THE GROUP (A): 5.5600 27.8420 48.7160 REMARK 3 T TENSOR REMARK 3 T11: -0.1797 T22: -0.1559 REMARK 3 T33: -0.1702 T12: 0.0013 REMARK 3 T13: 0.0083 T23: 0.0034 REMARK 3 L TENSOR REMARK 3 L11: 1.0497 L22: 1.3287 REMARK 3 L33: 1.1686 L12: 0.2797 REMARK 3 L13: -0.2511 L23: -0.4432 REMARK 3 S TENSOR REMARK 3 S11: 0.0392 S12: -0.0252 S13: 0.0780 REMARK 3 S21: 0.0191 S22: 0.0006 S23: -0.0441 REMARK 3 S31: -0.0072 S32: 0.0386 S33: -0.0397 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : L 107 L 211 REMARK 3 ORIGIN FOR THE GROUP (A): 0.8020 20.7210 12.8020 REMARK 3 T TENSOR REMARK 3 T11: -0.0482 T22: 0.0666 REMARK 3 T33: -0.1241 T12: 0.0444 REMARK 3 T13: -0.0015 T23: 0.0385 REMARK 3 L TENSOR REMARK 3 L11: 1.8219 L22: 2.8073 REMARK 3 L33: 3.1058 L12: 1.5706 REMARK 3 L13: 0.9280 L23: 1.7819 REMARK 3 S TENSOR REMARK 3 S11: -0.0750 S12: 0.2831 S13: 0.0850 REMARK 3 S21: -0.4489 S22: 0.0711 S23: 0.1822 REMARK 3 S31: -0.2504 S32: -0.4603 S33: 0.0038 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2W9D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-JAN-09. REMARK 100 THE DEPOSITION ID IS D_1290037802. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUN-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX10.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : SI111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54085 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.570 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.57 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 70.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.38000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2HHO REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350, TRIS PH 8.0, PH 7.5 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 18.39200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.92600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.35500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.92600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.39200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.35500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 3780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.8 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, 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 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 GLU L 212 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 SER H 131 OG REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 THR H 135 CB OG1 CG2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 TYR H 52 C PRO H 53 N 0.123 REMARK 500 THR H 135 CA THR H 135 CB 0.438 REMARK 500 REMARK 500 REMARK: NULL 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 THR H 135 N - CA - CB ANGL. DEV. = 16.4 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 THR H 30 -87.51 -95.81 REMARK 500 LYS H 43 -89.83 -132.78 REMARK 500 ASN H 55 102.98 48.64 REMARK 500 TYR H 101 -111.51 54.65 REMARK 500 ALA H 132 -168.21 173.43 REMARK 500 ALA H 133 -63.21 -178.49 REMARK 500 GLN H 134 102.38 67.47 REMARK 500 SER H 162 -45.27 -148.96 REMARK 500 THR L 50 -48.25 74.74 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 H2019 DISTANCE = 6.32 ANGSTROMS REMARK 525 HOH L2034 DISTANCE = 6.28 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA H 251 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH H2028 O REMARK 620 2 HOH H2051 O 88.0 REMARK 620 3 HOH H2067 O 86.1 82.3 REMARK 620 4 HOH H2072 O 85.8 170.4 90.0 REMARK 620 5 HOH H2125 O 179.0 92.2 93.0 93.9 REMARK 620 6 HOH H2126 O 88.6 100.6 173.9 86.5 92.3 REMARK 620 N 1 2 3 4 5 REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA H 251 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2W9E RELATED DB: PDB REMARK 900 STRUCTURE OF ICSM 18 (ANTI-PRP THERAPEUTIC ANTIBODY) FAB FRAGMENT REMARK 900 COMPLEXED WITH HUMAN PRP FRAGMENT 119-231 DBREF 2W9D H 1 215 PDB 2W9D 2W9D 1 215 DBREF 2W9D L 1 212 PDB 2W9D 2W9D 1 212 SEQRES 1 H 215 GLU VAL GLN LEU GLN GLN SER GLY PRO GLU LEU VAL LYS SEQRES 2 H 215 PRO GLY SER SER VAL LYS ILE SER CYS LYS ALA SER ARG SEQRES 3 H 215 ASN THR PHE THR ASP TYR ASN LEU ASP TRP VAL LYS GLN SEQRES 4 H 215 SER HIS GLY LYS THR LEU GLU TRP ILE GLY ASN VAL TYR SEQRES 5 H 215 PRO ASN ASN GLY VAL THR GLY TYR ASN GLN LYS PHE ARG SEQRES 6 H 215 GLY LYS ALA THR LEU THR VAL ASP LYS SER SER SER THR SEQRES 7 H 215 ALA TYR MET GLU LEU HIS SER LEU THR SER GLU ASP SER SEQRES 8 H 215 ALA VAL TYR TYR CYS ALA LEU TYR TYR TYR ASP VAL SER SEQRES 9 H 215 TYR TRP GLY GLN GLY THR LEU VAL THR VAL SER SER ALA SEQRES 10 H 215 LYS THR THR PRO PRO SER VAL TYR PRO LEU ALA PRO GLY SEQRES 11 H 215 SER ALA ALA GLN THR SER MET VAL THR LEU GLY CYS LEU SEQRES 12 H 215 VAL LYS GLY TYR PHE PRO GLU PRO VAL THR VAL THR TRP SEQRES 13 H 215 ASN SER GLY SER LEU SER SER GLY VAL HIS THR PHE PRO SEQRES 14 H 215 ALA VAL LEU GLN SER ASP LEU TYR THR LEU SER SER SER SEQRES 15 H 215 VAL THR VAL PRO SER SER THR TRP PRO SER GLN SER VAL SEQRES 16 H 215 THR CYS ASN VAL ALA HIS PRO ALA SER SER THR LYS VAL SEQRES 17 H 215 ASP LYS LYS ILE THR PRO ARG SEQRES 1 L 212 PCA ILE VAL LEU THR GLN SER PRO ALA ILE MET SER ALA SEQRES 2 L 212 SER PRO GLY GLU LYS VAL THR MET THR CYS SER ALA SER SEQRES 3 L 212 SER SER VAL SER TYR MET HIS TRP TYR GLN GLN LYS SER SEQRES 4 L 212 GLY THR SER PRO LYS ARG TRP ILE TYR ASP THR SER LYS SEQRES 5 L 212 LEU ALA SER GLY VAL PRO ALA ARG PHE SER GLY SER GLY SEQRES 6 L 212 SER GLY THR SER TYR SER LEU THR ILE SER SER MET GLU SEQRES 7 L 212 ALA GLU ASP ALA ALA THR TYR PHE CYS HIS GLN TRP ARG SEQRES 8 L 212 SER ASN PRO TYR THR PHE GLY GLY GLY THR LYS LEU GLU SEQRES 9 L 212 ILE LYS ARG ALA ASP ALA ALA PRO THR VAL SER ILE PHE SEQRES 10 L 212 PRO PRO SER SER GLU GLN LEU THR SER GLY GLY ALA SER SEQRES 11 L 212 VAL VAL CYS PHE LEU ASN ASN PHE TYR PRO LYS ASP ILE SEQRES 12 L 212 ASN VAL LYS TRP LYS ILE ASP GLY SER GLU ARG GLN ASN SEQRES 13 L 212 GLY VAL LEU ASN SER TRP THR ASP GLN ASP SER LYS ASP SEQRES 14 L 212 SER THR TYR SER MET SER SER THR LEU THR LEU THR LYS SEQRES 15 L 212 ASP GLU TYR GLU ARG HIS ASN SER TYR THR CYS GLU ALA SEQRES 16 L 212 THR HIS LYS THR SER THR SER PRO ILE VAL LYS SER PHE SEQRES 17 L 212 ASN ARG ASN GLU MODRES 2W9D PCA L 1 GLU PYROGLUTAMIC ACID HET PCA L 1 8 HET CA H 251 1 HETNAM PCA PYROGLUTAMIC ACID HETNAM CA CALCIUM ION FORMUL 2 PCA C5 H7 N O3 FORMUL 3 CA CA 2+ FORMUL 4 HOH *667(H2 O) HELIX 1 1 GLN H 62 ARG H 65 5 4 HELIX 2 2 THR H 87 SER H 91 5 5 HELIX 3 3 SER H 158 SER H 160 5 3 HELIX 4 4 PRO H 202 SER H 205 5 4 HELIX 5 5 GLU L 78 ALA L 82 5 5 HELIX 6 6 SER L 120 SER L 126 1 7 HELIX 7 7 LYS L 182 HIS L 188 1 7 SHEET 1 HA 4 LEU H 4 GLN H 6 0 SHEET 2 HA 4 VAL H 18 ALA H 24 -1 O LYS H 23 N GLN H 5 SHEET 3 HA 4 ALA H 79 LEU H 83 -1 O ALA H 79 N CYS H 22 SHEET 4 HA 4 ALA H 68 VAL H 72 -1 O THR H 69 N GLU H 82 SHEET 1 HB 6 GLU H 10 VAL H 12 0 SHEET 2 HB 6 THR H 110 VAL H 114 1 O LEU H 111 N GLU H 10 SHEET 3 HB 6 ALA H 92 TYR H 100 -1 O ALA H 92 N VAL H 112 SHEET 4 HB 6 ASN H 33 GLN H 39 -1 O ASN H 33 N TYR H 99 SHEET 5 HB 6 LEU H 45 VAL H 51 -1 O GLU H 46 N LYS H 38 SHEET 6 HB 6 THR H 58 TYR H 60 -1 O GLY H 59 N ASN H 50 SHEET 1 HC 4 GLU H 10 VAL H 12 0 SHEET 2 HC 4 THR H 110 VAL H 114 1 O LEU H 111 N GLU H 10 SHEET 3 HC 4 ALA H 92 TYR H 100 -1 O ALA H 92 N VAL H 112 SHEET 4 HC 4 VAL H 103 TRP H 106 -1 O VAL H 103 N TYR H 100 SHEET 1 HD 4 SER H 123 LEU H 127 0 SHEET 2 HD 4 MET H 137 TYR H 147 -1 O GLY H 141 N LEU H 127 SHEET 3 HD 4 LEU H 176 PRO H 186 -1 O TYR H 177 N TYR H 147 SHEET 4 HD 4 VAL H 165 THR H 167 -1 O HIS H 166 N SER H 182 SHEET 1 HE 4 SER H 123 LEU H 127 0 SHEET 2 HE 4 MET H 137 TYR H 147 -1 O GLY H 141 N LEU H 127 SHEET 3 HE 4 LEU H 176 PRO H 186 -1 O TYR H 177 N TYR H 147 SHEET 4 HE 4 VAL H 171 GLN H 173 -1 O VAL H 171 N THR H 178 SHEET 1 HF 3 THR H 153 TRP H 156 0 SHEET 2 HF 3 THR H 196 HIS H 201 -1 O ASN H 198 N THR H 155 SHEET 3 HF 3 THR H 206 LYS H 211 -1 O THR H 206 N HIS H 201 SHEET 1 LA 4 LEU L 4 SER L 7 0 SHEET 2 LA 4 VAL L 19 ALA L 25 -1 O THR L 22 N SER L 7 SHEET 3 LA 4 SER L 69 ILE L 74 -1 O TYR L 70 N CYS L 23 SHEET 4 LA 4 PHE L 61 SER L 66 -1 O SER L 62 N THR L 73 SHEET 1 LB 6 ILE L 10 ALA L 13 0 SHEET 2 LB 6 THR L 101 ILE L 105 1 O LYS L 102 N MET L 11 SHEET 3 LB 6 ALA L 83 GLN L 89 -1 O ALA L 83 N LEU L 103 SHEET 4 LB 6 HIS L 33 GLN L 37 -1 O HIS L 33 N HIS L 88 SHEET 5 LB 6 LYS L 44 TYR L 48 -1 O LYS L 44 N GLN L 36 SHEET 6 LB 6 LYS L 52 LEU L 53 -1 O LYS L 52 N TYR L 48 SHEET 1 LC 4 ILE L 10 ALA L 13 0 SHEET 2 LC 4 THR L 101 ILE L 105 1 O LYS L 102 N MET L 11 SHEET 3 LC 4 ALA L 83 GLN L 89 -1 O ALA L 83 N LEU L 103 SHEET 4 LC 4 THR L 96 PHE L 97 -1 O THR L 96 N GLN L 89 SHEET 1 LD 4 THR L 113 PHE L 117 0 SHEET 2 LD 4 GLY L 128 PHE L 138 -1 O VAL L 132 N PHE L 117 SHEET 3 LD 4 TYR L 172 THR L 181 -1 O TYR L 172 N PHE L 138 SHEET 4 LD 4 VAL L 158 TRP L 162 -1 O LEU L 159 N THR L 177 SHEET 1 LE 4 SER L 152 ARG L 154 0 SHEET 2 LE 4 ASN L 144 ILE L 149 -1 O TRP L 147 N ARG L 154 SHEET 3 LE 4 SER L 190 THR L 196 -1 O THR L 192 N LYS L 148 SHEET 4 LE 4 ILE L 204 ASN L 209 -1 O ILE L 204 N ALA L 195 SSBOND 1 CYS H 22 CYS H 96 1555 1555 2.05 SSBOND 2 CYS H 142 CYS H 197 1555 1555 2.02 SSBOND 3 CYS L 23 CYS L 87 1555 1555 2.07 SSBOND 4 CYS L 133 CYS L 193 1555 1555 2.03 LINK C PCA L 1 N ILE L 2 1555 1555 1.33 LINK CA CA H 251 O HOH H2028 1555 1555 2.23 LINK CA CA H 251 O HOH H2051 1555 1555 2.33 LINK CA CA H 251 O HOH H2067 1555 1555 2.25 LINK CA CA H 251 O HOH H2072 1555 1555 2.10 LINK CA CA H 251 O HOH H2125 1555 1555 2.15 LINK CA CA H 251 O HOH H2126 1555 1555 2.76 CISPEP 1 PHE H 148 PRO H 149 0 -6.05 CISPEP 2 GLU H 150 PRO H 151 0 -3.27 CISPEP 3 TRP H 190 PRO H 191 0 7.78 CISPEP 4 SER L 7 PRO L 8 0 -3.62 CISPEP 5 ASN L 93 PRO L 94 0 5.47 CISPEP 6 TYR L 139 PRO L 140 0 2.51 SITE 1 AC1 6 HOH H2028 HOH H2051 HOH H2067 HOH H2072 SITE 2 AC1 6 HOH H2125 HOH H2126 CRYST1 36.784 84.710 127.852 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.027186 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011805 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007822 0.00000