HEADER PROTEIN BINDING 21-OCT-14 4D3C TITLE CRYSTAL STRUCTURE OF THE NK1 DOMAIN OF HGF IN COMPLEX WITH ANTI-HGF TITLE 2 MONOCLONAL ANTIBODY SFN68. COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEPATOCYTE GROWTH FACTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 23-210; COMPND 5 SYNONYM: HEPATOPOIETIN-A, SCATTER FACTOR, SF, NK1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: SFN68 FAB; COMPND 10 CHAIN: H; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: SFN68 FAB; COMPND 13 CHAIN: L SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: ORYCTOLAGUS CUNICULUS; SOURCE 9 ORGANISM_COMMON: RABBIT; SOURCE 10 ORGANISM_TAXID: 9986; SOURCE 11 OTHER_DETAILS: RABBIT/HUMAN CHIMERIC ANTIBODY; SOURCE 12 MOL_ID: 3; SOURCE 13 ORGANISM_SCIENTIFIC: ORYCTOLAGUS CUNICULUS; SOURCE 14 ORGANISM_COMMON: RABBIT; SOURCE 15 ORGANISM_TAXID: 9986; SOURCE 16 OTHER_DETAILS: RABBIT/HUMAN CHIMERIC ANTIBODY KEYWDS PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR Y.J.KANG,K.L.KIM,H.S.CHO,J.H.CHUNG REVDAT 3 20-DEC-23 4D3C 1 REMARK REVDAT 2 29-AUG-18 4D3C 1 JRNL REVDAT 1 13-JAN-16 4D3C 0 JRNL AUTH Y.J.KANG,K.L.KIM,H.S.CHO,J.H.CHUNG JRNL TITL A MECHANISTIC BASIS FOR CONVERTING A RECEPTOR TYROSINE JRNL TITL 2 KINASE AGONIST TO AN ANTAGONIST. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.62 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.62 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.79 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 25541 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.269 REMARK 3 R VALUE (WORKING SET) : 0.268 REMARK 3 FREE R VALUE : 0.298 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1347 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) : 2.62 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1586 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.58 REMARK 3 BIN R VALUE (WORKING SET) : 0.3960 REMARK 3 BIN FREE R VALUE SET COUNT : 92 REMARK 3 BIN FREE R VALUE : 0.4260 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4225 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 22 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 85.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.12000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : -1.11000 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): 0.511 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.328 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.318 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.560 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.909 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.879 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4329 ; 0.012 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 3967 ; 0.007 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5882 ; 1.456 ; 1.950 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9161 ; 0.835 ; 3.004 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 549 ; 6.150 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 172 ;34.490 ;24.360 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 691 ;15.563 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;15.611 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 655 ; 0.073 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4910 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 977 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 4D3C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-OCT-14. REMARK 100 THE DEPOSITION ID IS D_1290061983. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 93.15 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : NULL 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25541 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.620 REMARK 200 RESOLUTION RANGE LOW (A) : 29.790 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRIES 1JPT, 1NK1. REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.35650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.35650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 43.35150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 148.84600 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 43.35150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 148.84600 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 35.35650 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 43.35150 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 148.84600 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 35.35650 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 43.35150 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 148.84600 REMARK 290 SMTRY3 8 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 MET A 18 REMARK 465 GLY A 19 REMARK 465 SER A 20 REMARK 465 SER A 21 REMARK 465 HIS A 22 REMARK 465 HIS A 23 REMARK 465 HIS A 24 REMARK 465 HIS A 25 REMARK 465 HIS A 26 REMARK 465 HIS A 27 REMARK 465 SER A 28 REMARK 465 GLN A 29 REMARK 465 ASP A 30 REMARK 465 PRO A 31 REMARK 465 GLN A 32 REMARK 465 ARG A 33 REMARK 465 LYS A 34 REMARK 465 ARG A 35 REMARK 465 ARG A 36 REMARK 465 THR A 49 REMARK 465 LEU A 50 REMARK 465 ILE A 51 REMARK 465 LYS A 52 REMARK 465 ILE A 53 REMARK 465 ASP A 54 REMARK 465 PRO A 55 REMARK 465 ALA A 56 REMARK 465 LEU A 57 REMARK 465 LYS A 58 REMARK 465 ILE A 59 REMARK 465 LYS A 60 REMARK 465 THR A 61 REMARK 465 LYS A 62 REMARK 465 LYS A 63 REMARK 465 VAL A 64 REMARK 465 ASN A 65 REMARK 465 THR A 66 REMARK 465 ASP A 90 REMARK 465 LYS A 91 REMARK 465 ALA A 92 REMARK 465 ARG A 93 REMARK 465 LYS A 94 REMARK 465 GLN A 95 REMARK 465 SER A 106 REMARK 465 GLY A 107 REMARK 465 VAL A 108 REMARK 465 LYS A 109 REMARK 465 LYS A 110 REMARK 465 GLU A 111 REMARK 465 PHE A 112 REMARK 465 GLY A 113 REMARK 465 HIS A 114 REMARK 465 GLU A 115 REMARK 465 PHE A 116 REMARK 465 VAL A 209 REMARK 465 GLU A 210 REMARK 465 SER H 131 REMARK 465 ARG H 132 REMARK 465 SER H 133 REMARK 465 THR H 134 REMARK 465 SER H 135 REMARK 465 GLU H 136 REMARK 465 LYS H 217 REMARK 465 TYR H 218 REMARK 465 PHE L 210 REMARK 465 ASN L 211 REMARK 465 ARG L 212 REMARK 465 GLY L 213 REMARK 465 GLU L 214 REMARK 465 CYS L 215 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 O LEU L 33 O GLY L 50 1.83 REMARK 500 REMARK 500 REMARK: NULL 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 148 CG TYR H 148 CD1 -0.118 REMARK 500 CYS H 199 CB CYS H 199 SG -0.102 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 GLY L 77 N - CA - C ANGL. DEV. = -17.8 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 PRO A 100 39.54 -92.15 REMARK 500 ASN A 127 34.38 -85.09 REMARK 500 LYS A 137 22.87 -150.21 REMARK 500 SER A 141 37.42 -142.24 REMARK 500 SER A 161 72.06 -105.93 REMARK 500 ASP A 171 78.09 58.03 REMARK 500 GLU A 174 -137.14 50.57 REMARK 500 SER H 30 -48.64 -134.51 REMARK 500 THR H 31 -5.45 91.82 REMARK 500 VAL H 64 -31.70 -141.76 REMARK 500 LEU H 100 -60.70 -124.90 REMARK 500 THR H 194 -62.31 -98.06 REMARK 500 SER L 30 72.03 60.95 REMARK 500 ASN L 31 13.35 51.67 REMARK 500 LEU L 47 -63.08 -103.69 REMARK 500 ALA L 83 105.46 -57.93 REMARK 500 SER L 94 143.83 -171.62 REMARK 500 ALA L 97 135.92 -175.79 REMARK 500 ASN L 139 78.86 51.13 REMARK 500 ASP L 152 53.14 32.83 REMARK 500 ASN L 153 24.40 -155.89 REMARK 500 LEU L 155 25.33 45.94 REMARK 500 GLN L 156 105.77 -55.54 REMARK 500 REMARK 500 REMARK: NULL DBREF 4D3C A 32 210 UNP P14210 HGF_HUMAN 32 210 DBREF 4D3C H 1 218 PDB 4D3C 4D3C 1 218 DBREF 4D3C L 1 215 PDB 4D3C 4D3C 1 215 SEQADV 4D3C MET A 18 UNP P14210 EXPRESSION TAG SEQADV 4D3C GLY A 19 UNP P14210 EXPRESSION TAG SEQADV 4D3C SER A 20 UNP P14210 EXPRESSION TAG SEQADV 4D3C SER A 21 UNP P14210 EXPRESSION TAG SEQADV 4D3C HIS A 22 UNP P14210 EXPRESSION TAG SEQADV 4D3C HIS A 23 UNP P14210 EXPRESSION TAG SEQADV 4D3C HIS A 24 UNP P14210 EXPRESSION TAG SEQADV 4D3C HIS A 25 UNP P14210 EXPRESSION TAG SEQADV 4D3C HIS A 26 UNP P14210 EXPRESSION TAG SEQADV 4D3C HIS A 27 UNP P14210 EXPRESSION TAG SEQADV 4D3C SER A 28 UNP P14210 EXPRESSION TAG SEQADV 4D3C GLN A 29 UNP P14210 EXPRESSION TAG SEQADV 4D3C ASP A 30 UNP P14210 EXPRESSION TAG SEQADV 4D3C PRO A 31 UNP P14210 EXPRESSION TAG SEQADV 4D3C GLY A 134 UNP P14210 ARG 134 ENGINEERED MUTATION SEQRES 1 A 193 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER GLN ASP SEQRES 2 A 193 PRO GLN ARG LYS ARG ARG ASN THR ILE HIS GLU PHE LYS SEQRES 3 A 193 LYS SER ALA LYS THR THR LEU ILE LYS ILE ASP PRO ALA SEQRES 4 A 193 LEU LYS ILE LYS THR LYS LYS VAL ASN THR ALA ASP GLN SEQRES 5 A 193 CYS ALA ASN ARG CYS THR ARG ASN LYS GLY LEU PRO PHE SEQRES 6 A 193 THR CYS LYS ALA PHE VAL PHE ASP LYS ALA ARG LYS GLN SEQRES 7 A 193 CYS LEU TRP PHE PRO PHE ASN SER MET SER SER GLY VAL SEQRES 8 A 193 LYS LYS GLU PHE GLY HIS GLU PHE ASP LEU TYR GLU ASN SEQRES 9 A 193 LYS ASP TYR ILE ARG ASN CYS ILE ILE GLY LYS GLY GLY SEQRES 10 A 193 SER TYR LYS GLY THR VAL SER ILE THR LYS SER GLY ILE SEQRES 11 A 193 LYS CYS GLN PRO TRP SER SER MET ILE PRO HIS GLU HIS SEQRES 12 A 193 SER PHE LEU PRO SER SER TYR ARG GLY LYS ASP LEU GLN SEQRES 13 A 193 GLU ASN TYR CYS ARG ASN PRO ARG GLY GLU GLU GLY GLY SEQRES 14 A 193 PRO TRP CYS PHE THR SER ASN PRO GLU VAL ARG TYR GLU SEQRES 15 A 193 VAL CYS ASP ILE PRO GLN CYS SER GLU VAL GLU SEQRES 1 H 218 GLN GLN GLN LEU VAL GLU SER GLY GLY ARG LEU VAL ASN SEQRES 2 H 218 PRO GLY GLU SER LEU THR LEU THR CYS LYS ALA SER GLY SEQRES 3 H 218 PHE THR PHE SER THR TYR TYR MET SER TRP VAL ARG GLN SEQRES 4 H 218 ALA PRO GLY LYS GLY LEU GLU TRP ILE GLY TYR ILE GLY SEQRES 5 H 218 THR SER SER GLY THR THR TYR TYR ALA ASN SER VAL LYS SEQRES 6 H 218 GLY ARG PHE THR ILE SER SER ASP ASN ALA GLN ASN THR SEQRES 7 H 218 VAL PHE LEU GLN MET THR SER LEU THR ASP SER ASP THR SEQRES 8 H 218 ALA THR TYR PHE CYS ALA ARG GLY LEU GLY ARG ILE ASN SEQRES 9 H 218 LEU TRP GLY PRO GLY THR LEU VAL THR VAL SER SER ALA SEQRES 10 H 218 SER THR LYS GLY PRO SER VAL PHE PRO LEU ALA PRO CYS SEQRES 11 H 218 SER ARG SER THR SER GLU SER THR ALA ALA LEU GLY CYS SEQRES 12 H 218 LEU VAL LYS ASP TYR PHE PRO GLU PRO VAL THR VAL SER SEQRES 13 H 218 TRP ASN SER GLY ALA LEU THR SER GLY VAL HIS THR PHE SEQRES 14 H 218 PRO ALA VAL LEU GLN SER SER GLY LEU TYR SER LEU SER SEQRES 15 H 218 SER VAL VAL THR VAL PRO SER SER SER LEU GLY THR LYS SEQRES 16 H 218 THR TYR THR CYS ASN VAL ASP HIS LYS PRO SER ASN THR SEQRES 17 H 218 LYS VAL ASP LYS ARG VAL GLU SER LYS TYR SEQRES 1 L 215 GLU LEU ASP LEU THR GLN THR PRO SER SER VAL SER ALA SEQRES 2 L 215 ALA VAL GLY GLY THR VAL THR ILE ASN CYS GLN ALA SER SEQRES 3 L 215 GLN SER VAL SER ASN LEU LEU ALA TRP TYR GLN GLN LYS SEQRES 4 L 215 PRO GLY GLN PRO PRO LYS LEU LEU ILE TYR GLY ALA SER SEQRES 5 L 215 ASN LEU GLU SER GLY VAL PRO SER ARG PHE ARG GLY SER SEQRES 6 L 215 GLY SER GLY THR GLU PHE THR LEU THR ILE SER GLY MET SEQRES 7 L 215 LYS ALA GLU ASP ALA ALA THR TYR TYR CYS GLN SER GLY SEQRES 8 L 215 TYR TYR SER ALA GLY ALA THR PHE GLY ALA GLY THR ASN SEQRES 9 L 215 VAL GLU ILE LYS ARG THR VAL ALA ALA PRO SER VAL PHE SEQRES 10 L 215 ILE PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR SEQRES 11 L 215 ALA SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG SEQRES 12 L 215 GLU ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SEQRES 13 L 215 SER GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SER SEQRES 14 L 215 LYS ASP SER THR TYR SER LEU SER SER THR LEU THR LEU SEQRES 15 L 215 SER LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS SEQRES 16 L 215 GLU VAL THR HIS GLN GLY LEU SER SER PRO VAL THR LYS SEQRES 17 L 215 SER PHE ASN ARG GLY GLU CYS FORMUL 4 HOH *22(H2 O) HELIX 1 1 ALA A 67 ARG A 76 1 10 HELIX 2 2 ASP A 123 ILE A 125 5 3 HELIX 3 3 ASN H 74 GLN H 76 5 3 HELIX 4 4 THR H 87 THR H 91 5 5 HELIX 5 5 SER H 159 ALA H 161 5 3 HELIX 6 6 SER H 190 GLY H 193 5 4 HELIX 7 7 LYS L 79 ALA L 83 5 5 HELIX 8 8 SER L 122 SER L 128 1 7 HELIX 9 9 LYS L 184 HIS L 190 1 7 SHEET 1 AA 4 PHE A 42 SER A 45 0 SHEET 2 AA 4 LEU A 118 ASN A 121 -1 O LEU A 118 N SER A 45 SHEET 3 AA 4 ALA A 86 VAL A 88 -1 O PHE A 87 N TYR A 119 SHEET 4 AA 4 LEU A 97 PHE A 99 -1 O LEU A 97 N VAL A 88 SHEET 1 AB 2 TRP A 188 PHE A 190 0 SHEET 2 AB 2 TYR A 198 VAL A 200 -1 O GLU A 199 N CYS A 189 SHEET 1 HA 4 GLN H 3 SER H 7 0 SHEET 2 HA 4 LEU H 18 SER H 25 -1 O THR H 21 N SER H 7 SHEET 3 HA 4 THR H 78 MET H 83 -1 O VAL H 79 N CYS H 22 SHEET 4 HA 4 PHE H 68 ASP H 73 -1 O THR H 69 N GLN H 82 SHEET 1 HB 4 LEU H 11 VAL H 12 0 SHEET 2 HB 4 THR H 110 VAL H 114 1 O THR H 113 N VAL H 12 SHEET 3 HB 4 ALA H 92 ARG H 98 -1 O ALA H 92 N VAL H 112 SHEET 4 HB 4 LEU H 105 TRP H 106 -1 O LEU H 105 N ARG H 98 SHEET 1 HC 6 LEU H 11 VAL H 12 0 SHEET 2 HC 6 THR H 110 VAL H 114 1 O THR H 113 N VAL H 12 SHEET 3 HC 6 ALA H 92 ARG H 98 -1 O ALA H 92 N VAL H 112 SHEET 4 HC 6 TYR H 33 GLN H 39 -1 O SER H 35 N ALA H 97 SHEET 5 HC 6 LEU H 45 GLY H 52 -1 O GLU H 46 N ARG H 38 SHEET 6 HC 6 THR H 58 TYR H 60 -1 O TYR H 59 N TYR H 50 SHEET 1 HD 2 LEU H 105 TRP H 106 0 SHEET 2 HD 2 ALA H 92 ARG H 98 -1 O ARG H 98 N LEU H 105 SHEET 1 HE 4 SER H 123 LEU H 127 0 SHEET 2 HE 4 THR H 138 TYR H 148 -1 O GLY H 142 N LEU H 127 SHEET 3 HE 4 TYR H 179 PRO H 188 -1 O TYR H 179 N TYR H 148 SHEET 4 HE 4 VAL H 172 LEU H 173 1 O VAL H 172 N SER H 180 SHEET 1 HF 4 SER H 123 LEU H 127 0 SHEET 2 HF 4 THR H 138 TYR H 148 -1 O GLY H 142 N LEU H 127 SHEET 3 HF 4 TYR H 179 PRO H 188 -1 O TYR H 179 N TYR H 148 SHEET 4 HF 4 VAL H 166 THR H 168 -1 O HIS H 167 N VAL H 184 SHEET 1 HG 2 VAL H 172 LEU H 173 0 SHEET 2 HG 2 TYR H 179 PRO H 188 1 O SER H 180 N VAL H 172 SHEET 1 HH 3 VAL H 153 TRP H 157 0 SHEET 2 HH 3 THR H 198 HIS H 203 -1 O ASN H 200 N SER H 156 SHEET 3 HH 3 THR H 208 ARG H 213 -1 O THR H 208 N HIS H 203 SHEET 1 LA 4 LEU L 4 THR L 7 0 SHEET 2 LA 4 VAL L 19 ALA L 25 -1 O ASN L 22 N THR L 7 SHEET 3 LA 4 GLU L 70 ILE L 75 -1 O PHE L 71 N CYS L 23 SHEET 4 LA 4 PHE L 62 SER L 67 -1 O ARG L 63 N THR L 74 SHEET 1 LB 4 SER L 10 ALA L 13 0 SHEET 2 LB 4 THR L 103 ILE L 107 1 O ASN L 104 N VAL L 11 SHEET 3 LB 4 THR L 85 GLY L 91 -1 O TYR L 86 N THR L 103 SHEET 4 LB 4 ALA L 97 PHE L 99 -1 O THR L 98 N SER L 90 SHEET 1 LC 6 SER L 10 ALA L 13 0 SHEET 2 LC 6 THR L 103 ILE L 107 1 O ASN L 104 N VAL L 11 SHEET 3 LC 6 THR L 85 GLY L 91 -1 O TYR L 86 N THR L 103 SHEET 4 LC 6 ALA L 34 GLN L 38 -1 O ALA L 34 N GLN L 89 SHEET 5 LC 6 LYS L 45 TYR L 49 -1 O LYS L 45 N GLN L 37 SHEET 6 LC 6 ASN L 53 LEU L 54 -1 O ASN L 53 N TYR L 49 SHEET 1 LD 2 ALA L 97 PHE L 99 0 SHEET 2 LD 2 THR L 85 GLY L 91 -1 O SER L 90 N THR L 98 SHEET 1 LE 4 SER L 115 ILE L 118 0 SHEET 2 LE 4 THR L 130 PHE L 140 -1 O LEU L 136 N PHE L 117 SHEET 3 LE 4 TYR L 174 SER L 183 -1 O TYR L 174 N PHE L 140 SHEET 4 LE 4 SER L 160 VAL L 164 -1 O GLN L 161 N THR L 179 SHEET 1 LF 3 LYS L 146 LYS L 150 0 SHEET 2 LF 3 ALA L 194 THR L 198 -1 O ALA L 194 N LYS L 150 SHEET 3 LF 3 VAL L 206 LYS L 208 -1 O VAL L 206 N VAL L 197 SSBOND 1 CYS A 70 CYS A 96 1555 1555 2.13 SSBOND 2 CYS A 74 CYS A 84 1555 1555 2.07 SSBOND 3 CYS A 128 CYS A 206 1555 1555 2.07 SSBOND 4 CYS A 149 CYS A 189 1555 1555 2.02 SSBOND 5 CYS A 177 CYS A 201 1555 1555 2.05 SSBOND 6 CYS H 22 CYS H 96 1555 1555 2.07 SSBOND 7 CYS H 143 CYS H 199 1555 1555 2.06 SSBOND 8 CYS L 23 CYS L 88 1555 1555 2.09 SSBOND 9 CYS L 135 CYS L 195 1555 1555 2.01 CISPEP 1 ILE A 156 PRO A 157 0 -1.23 CISPEP 2 PHE H 29 SER H 30 0 -7.74 CISPEP 3 SER H 30 THR H 31 0 -17.42 CISPEP 4 PHE H 149 PRO H 150 0 -6.08 CISPEP 5 GLU H 151 PRO H 152 0 -2.73 CISPEP 6 THR L 7 PRO L 8 0 -2.24 CISPEP 7 SER L 94 ALA L 95 0 4.79 CISPEP 8 TYR L 141 PRO L 142 0 -2.23 CISPEP 9 ASP L 152 ASN L 153 0 1.88 CRYST1 86.703 297.692 70.713 90.00 90.00 90.00 C 2 2 21 8 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 0.011534 0.000000 0.000000 0.00000 SCALE2 0.000000 0.003359 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014142 0.00000