HEADER HYDROLASE/HYDROLASE INHIBITOR 10-NOV-16 5PB1 TITLE CRYSTAL STRUCTURE OF FACTOR VIIA IN COMPLEX WITH TITLE 2 BENZENECARBOXIMIDAMIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: COAGULATION FACTOR VII LIGHT CHAIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROCONVERTIN,SERUM PROTHROMBIN CONVERSION ACCELERATOR,SPCA; COMPND 5 EC: 3.4.21.21; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: COAGULATION FACTOR VII HEAVY CHAIN; COMPND 9 CHAIN: D; COMPND 10 SYNONYM: PROCONVERTIN,SERUM PROTHROMBIN CONVERSION ACCELERATOR,SPCA; COMPND 11 EC: 3.4.21.21; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: F7; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: F7; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 17 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 18 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS GLYCOPROTEIN, HYDROLASE, SERINE PROTEASE, PLASMA, BLOOD COAGULATION KEYWDS 2 FACTOR, PROTEIN INHIBITOR COMPLEX, CALCIUM-BINDING, HYDROLASE- KEYWDS 3 HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.STIHLE,A.MAYWEG,S.ROEVER,M.G.RUDOLPH REVDAT 5 03-APR-24 5PB1 1 REMARK REVDAT 4 17-NOV-21 5PB1 1 REMARK REVDAT 3 18-AUG-21 5PB1 1 COMPND REMARK HET FORMUL REVDAT 3 2 1 ATOM REVDAT 2 21-FEB-18 5PB1 1 REMARK REVDAT 1 21-JUN-17 5PB1 0 JRNL AUTH A.MAYWEG,S.ROEVER,M.G.RUDOLPH JRNL TITL CRYSTAL STRUCTURE OF A FACTOR VIIA COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.79 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 41238 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) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2181 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3019 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.84 REMARK 3 BIN R VALUE (WORKING SET) : 0.2170 REMARK 3 BIN FREE R VALUE SET COUNT : 168 REMARK 3 BIN FREE R VALUE : 0.2440 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2364 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 64 REMARK 3 SOLVENT ATOMS : 378 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.49 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.96000 REMARK 3 B22 (A**2) : -0.96000 REMARK 3 B33 (A**2) : 1.91000 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): 0.115 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.109 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.072 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.407 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2616 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1798 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3591 ; 1.318 ; 1.979 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4376 ; 0.871 ; 3.004 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 346 ; 5.978 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 109 ;26.037 ;22.752 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 426 ;12.550 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;20.085 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 395 ; 0.081 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2900 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 538 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 423 ; 0.210 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1875 ; 0.205 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1203 ; 0.171 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1419 ; 0.079 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 303 ; 0.155 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 6 ; 0.100 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 2 ; 0.086 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 17 ; 0.228 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 23 ; 0.209 ; 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): 1659 ; 0.987 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 651 ; 0.167 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2590 ; 1.539 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1119 ; 2.058 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 980 ; 3.063 ; 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 5PB1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-DEC-16. REMARK 100 THE DEPOSITION ID IS D_1001400437. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUL-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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 : BRUKER AXS MICROSTAR REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51285 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.09900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.61000 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: PHASER REMARK 200 STARTING MODEL: INHOUSE MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16 MG/ML PROTEIN IN 20MM TRIS/HCL PH REMARK 280 8.4, 5 MM BENZAMIDINE, 0.1 M NACL, 50 MM CACL2 MIXED 1+1 WITH 32- REMARK 280 35% AMMONIUM SULPHATE, 2% PEG 4000, 0.1 M BICINE-NAOH PH 8.5, 15% REMARK 280 GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 58.98050 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 47.83800 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 47.83800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 29.49025 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 47.83800 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 47.83800 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 88.47075 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 47.83800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.83800 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 29.49025 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 47.83800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.83800 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 88.47075 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 58.98050 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: A, D 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH D 901 LIES ON A SPECIAL POSITION. 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 ASN A 205 REMARK 465 ALA A 206 REMARK 465 SER A 207 REMARK 465 LYS A 208 REMARK 465 PRO A 209 REMARK 465 GLN A 210 REMARK 465 GLY A 211 REMARK 465 ARG A 212 REMARK 465 LYS D 376 REMARK 465 VAL D 377 REMARK 465 GLY D 378 REMARK 465 ASP D 379 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 ARG D 375 CG CD NE CZ NH1 NH2 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 OG1 THR D 327 O HOH D 601 2.06 REMARK 500 O HOH D 608 O HOH D 870 2.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 448 O HOH D 878 7555 2.06 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 CYS D 238 CA - CB - SG ANGL. DEV. = 7.4 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 GLN A 160 -105.79 -119.57 REMARK 500 THR A 168 42.42 -92.50 REMARK 500 LEU D 237 -61.74 -107.89 REMARK 500 HIS D 271 -60.74 -140.83 REMARK 500 THR D 332 -57.19 -120.79 REMARK 500 SER D 423 -66.16 -124.07 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 D 915 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH D 916 DISTANCE = 5.98 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 D 501 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU D 270 OE1 REMARK 620 2 ASP D 272 O 85.7 REMARK 620 3 GLU D 275 O 160.6 84.8 REMARK 620 4 GLU D 280 OE2 99.5 168.8 93.0 REMARK 620 5 HOH D 634 O 82.8 102.1 82.7 88.5 REMARK 620 6 HOH D 829 O 82.3 88.9 114.4 82.0 160.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA D 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 D 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 D 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 D 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 D 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL D 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL D 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BEN D 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 D 509 DBREF 5PB1 A 149 212 UNP P08709 FA7_HUMAN 149 212 DBREF 5PB1 D 213 466 UNP P08709 FA7_HUMAN 213 466 SEQRES 1 A 64 LEU ILE CYS VAL ASN GLU ASN GLY GLY CYS GLU GLN TYR SEQRES 2 A 64 CYS SER ASP HIS THR GLY THR LYS ARG SER CYS ARG CYS SEQRES 3 A 64 HIS GLU GLY TYR SER LEU LEU ALA ASP GLY VAL SER CYS SEQRES 4 A 64 THR PRO THR VAL GLU TYR PRO CYS GLY LYS ILE PRO ILE SEQRES 5 A 64 LEU GLU LYS ARG ASN ALA SER LYS PRO GLN GLY ARG SEQRES 1 D 254 ILE VAL GLY GLY LYS VAL CYS PRO LYS GLY GLU CYS PRO SEQRES 2 D 254 TRP GLN VAL LEU LEU LEU VAL ASN GLY ALA GLN LEU CYS SEQRES 3 D 254 GLY GLY THR LEU ILE ASN THR ILE TRP VAL VAL SER ALA SEQRES 4 D 254 ALA HIS CYS PHE ASP LYS ILE LYS ASN TRP ARG ASN LEU SEQRES 5 D 254 ILE ALA VAL LEU GLY GLU HIS ASP LEU SER GLU HIS ASP SEQRES 6 D 254 GLY ASP GLU GLN SER ARG ARG VAL ALA GLN VAL ILE ILE SEQRES 7 D 254 PRO SER THR TYR VAL PRO GLY THR THR ASN HIS ASP ILE SEQRES 8 D 254 ALA LEU LEU ARG LEU HIS GLN PRO VAL VAL LEU THR ASP SEQRES 9 D 254 HIS VAL VAL PRO LEU CYS LEU PRO GLU ARG THR PHE SER SEQRES 10 D 254 GLU ARG THR LEU ALA PHE VAL ARG PHE SER LEU VAL SER SEQRES 11 D 254 GLY TRP GLY GLN LEU LEU ASP ARG GLY ALA THR ALA LEU SEQRES 12 D 254 GLU LEU MHO VAL LEU ASN VAL PRO ARG LEU MET THR GLN SEQRES 13 D 254 ASP CYS LEU GLN GLN SER ARG LYS VAL GLY ASP SER PRO SEQRES 14 D 254 ASN ILE THR GLU TYR MET PHE CYS ALA GLY TYR SER ASP SEQRES 15 D 254 GLY SER LYS ASP SER CYS LYS GLY ASP SER GLY GLY PRO SEQRES 16 D 254 HIS ALA THR HIS TYR ARG GLY THR TRP TYR LEU THR GLY SEQRES 17 D 254 ILE VAL SER TRP GLY GLN GLY CYS ALA THR VAL GLY HIS SEQRES 18 D 254 PHE GLY VAL TYR THR ARG VAL SER GLN TYR ILE GLU TRP SEQRES 19 D 254 LEU GLN LYS LEU MET ARG SER GLU PRO ARG PRO GLY VAL SEQRES 20 D 254 LEU LEU ARG ALA PRO PHE PRO MODRES 5PB1 MHO D 358 MET MODIFIED RESIDUE HET MHO D 358 9 HET SO4 A 301 5 HET GOL A 302 6 HET GOL A 303 6 HET CA D 501 1 HET SO4 D 502 5 HET SO4 D 503 5 HET SO4 D 504 5 HET SO4 D 505 5 HET GOL D 506 6 HET GOL D 507 6 HET BEN D 508 9 HET SO4 D 509 5 HETNAM MHO S-OXYMETHIONINE HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETNAM CA CALCIUM ION HETNAM BEN BENZAMIDINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 MHO C5 H11 N O3 S FORMUL 3 SO4 6(O4 S 2-) FORMUL 4 GOL 4(C3 H8 O3) FORMUL 6 CA CA 2+ FORMUL 13 BEN C7 H8 N2 FORMUL 15 HOH *378(H2 O) HELIX 1 AA1 ASN A 153 CYS A 158 5 6 HELIX 2 AA2 ILE A 198 ARG A 204 1 7 HELIX 3 AA3 ALA D 251 ASP D 256 5 6 HELIX 4 AA4 ASN D 260 ARG D 262 5 3 HELIX 5 AA5 GLU D 325 THR D 332 1 8 HELIX 6 AA6 LEU D 333 VAL D 336 5 4 HELIX 7 AA7 MET D 366 SER D 374 1 9 HELIX 8 AA8 TYR D 443 ARG D 452 1 10 SHEET 1 AA1 2 TYR A 161 HIS A 165 0 SHEET 2 AA1 2 LYS A 169 ARG A 173 -1 O ARG A 173 N TYR A 161 SHEET 1 AA2 2 TYR A 178 LEU A 180 0 SHEET 2 AA2 2 CYS A 187 PRO A 189 -1 O THR A 188 N SER A 179 SHEET 1 AA3 8 LYS D 217 VAL D 218 0 SHEET 2 AA3 8 MHO D 358 LEU D 365 -1 O VAL D 359 N LYS D 217 SHEET 3 AA3 8 MET D 387 ALA D 390 -1 O CYS D 389 N LEU D 365 SHEET 4 AA3 8 GLY D 435 ARG D 439 -1 O TYR D 437 N PHE D 388 SHEET 5 AA3 8 THR D 415 TRP D 424 -1 N TRP D 424 O VAL D 436 SHEET 6 AA3 8 PRO D 407 TYR D 412 -1 N TYR D 412 O THR D 415 SHEET 7 AA3 8 PHE D 338 GLY D 343 -1 N LEU D 340 O ALA D 409 SHEET 8 AA3 8 MHO D 358 LEU D 365 -1 O VAL D 362 N SER D 339 SHEET 1 AA4 8 LEU D 460 ALA D 463 0 SHEET 2 AA4 8 GLN D 281 PRO D 291 1 N VAL D 288 O LEU D 461 SHEET 3 AA4 8 ALA D 304 LEU D 308 -1 O LEU D 305 N ILE D 289 SHEET 4 AA4 8 TRP D 247 SER D 250 -1 N VAL D 248 O LEU D 306 SHEET 5 AA4 8 ALA D 235 ASN D 244 -1 N THR D 241 O VAL D 249 SHEET 6 AA4 8 GLN D 227 VAL D 232 -1 N LEU D 230 O LEU D 237 SHEET 7 AA4 8 LEU D 264 LEU D 268 -1 O ILE D 265 N LEU D 231 SHEET 8 AA4 8 GLN D 281 PRO D 291 -1 O ARG D 283 N ALA D 266 SSBOND 1 CYS A 151 CYS A 162 1555 1555 2.04 SSBOND 2 CYS A 158 CYS A 172 1555 1555 2.03 SSBOND 3 CYS A 174 CYS A 187 1555 1555 2.09 SSBOND 4 CYS A 195 CYS D 322 1555 1555 2.06 SSBOND 5 CYS D 219 CYS D 224 1555 1555 2.09 SSBOND 6 CYS D 238 CYS D 254 1555 1555 2.00 SSBOND 7 CYS D 370 CYS D 389 1555 1555 2.09 SSBOND 8 CYS D 400 CYS D 428 1555 1555 2.03 LINK C LEU D 357 N MHO D 358 1555 1555 1.33 LINK C MHO D 358 N VAL D 359 1555 1555 1.33 LINK OE1 GLU D 270 CA CA D 501 1555 1555 2.32 LINK O ASP D 272 CA CA D 501 1555 1555 2.35 LINK O GLU D 275 CA CA D 501 1555 1555 2.25 LINK OE2 GLU D 280 CA CA D 501 1555 1555 2.35 LINK CA CA D 501 O HOH D 634 1555 1555 2.33 LINK CA CA D 501 O HOH D 829 1555 1555 2.37 CISPEP 1 PHE D 465 PRO D 466 0 -1.73 SITE 1 AC1 5 PRO A 189 THR A 190 VAL A 191 HOH A 411 SITE 2 AC1 5 HOH A 426 SITE 1 AC2 8 LYS A 197 ILE A 198 LEU A 201 GLU A 202 SITE 2 AC2 8 TRP D 416 GOL D 506 HOH D 607 HOH D 752 SITE 1 AC3 5 CYS A 174 SER A 179 LEU A 180 HOH A 413 SITE 2 AC3 5 GLU D 454 SITE 1 AC4 6 GLU D 270 ASP D 272 GLU D 275 GLU D 280 SITE 2 AC4 6 HOH D 634 HOH D 829 SITE 1 AC5 4 ARG D 283 ARG D 284 HIS D 309 GLN D 310 SITE 1 AC6 6 THR D 315 ASP D 316 HIS D 317 HOH D 740 SITE 2 AC6 6 HOH D 763 HOH D 797 SITE 1 AC7 7 MET D 366 THR D 367 ARG D 439 HOH D 630 SITE 2 AC7 7 HOH D 712 HOH D 733 HOH D 826 SITE 1 AC8 5 GLN D 281 VAL D 313 THR D 315 HOH D 655 SITE 2 AC8 5 HOH D 734 SITE 1 AC9 7 ILE A 198 GOL A 302 LYS D 217 GLU D 223 SITE 2 AC9 7 LEU D 340 TRP D 416 HOH D 608 SITE 1 AD1 5 SER D 374 TRP D 424 GLN D 426 HIS D 433 SITE 2 AD1 5 PHE D 434 SITE 1 AD2 10 ASP D 398 SER D 399 SER D 404 VAL D 422 SITE 2 AD2 10 SER D 423 TRP D 424 GLY D 425 GLY D 427 SITE 3 AD2 10 GLY D 435 HOH D 700 SITE 1 AD3 6 HIS D 253 LYS D 401 GLY D 402 SER D 404 SITE 2 AD3 6 HOH D 690 HOH D 739 CRYST1 95.676 95.676 117.961 90.00 90.00 90.00 P 41 21 2 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 0.010452 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010452 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008477 0.00000