HEADER HYDROLASE INHIBITOR 23-JAN-12 4AFX TITLE CRYSTAL STRUCTURE OF THE REACTIVE LOOP CLEAVED ZPI IN I2 SPACE GROUP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN Z DEPENDENT PROTEASE INHIBITOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 23-408; COMPND 5 SYNONYM: PZ-DEPENDENT PROTEASE INHIBITOR, PZI, SERPIN A10; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 OTHER_DETAILS: REACTIVE LOOP CLEAVED ZPI; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: PROTEIN Z DEPENDENT PROTEASE INHIBITOR; COMPND 11 CHAIN: B; COMPND 12 FRAGMENT: RESIDUES 409-444; COMPND 13 SYNONYM: PZ-DEPENDENT PROTEASE INHIBITOR, PZI, SERPIN A10; COMPND 14 ENGINEERED: YES; COMPND 15 MUTATION: YES; COMPND 16 OTHER_DETAILS: REACTIVE LOOP CLEAVED ZPI 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: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: STAR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PSUMO3; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PSUMO3-HZPI-Y387R; SOURCE 12 MOL_ID: 2; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_VARIANT: STAR; SOURCE 20 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 21 EXPRESSION_SYSTEM_VECTOR: PSUMO3; SOURCE 22 EXPRESSION_SYSTEM_PLASMID: PSUMO3-HZPI-Y387R KEYWDS HYDROLASE INHIBITOR, SERPIN, PROTEIN Z DEPENDENT INHIBITOR, KEYWDS 2 COAGULATION EXPDTA X-RAY DIFFRACTION AUTHOR A.ZHOU,Y.YAN,Z.WEI REVDAT 3 20-DEC-23 4AFX 1 REMARK LINK REVDAT 2 12-JUN-19 4AFX 1 JRNL REMARK REVDAT 1 09-JAN-13 4AFX 0 JRNL AUTH X.HUANG,Y.YAN,Y.TU,J.GATTI,G.J.J.BROZE,A.ZHOU,S.T.OLSON JRNL TITL STRUCTURAL BASIS FOR CATALYTIC ACTIVATION OF PROTEIN JRNL TITL 2 Z-DEPENDENT PROTEASE INHIBITOR (ZPI) BY PROTEIN Z. JRNL REF BLOOD V. 120 1726 2012 JRNL REFN ISSN 0006-4971 JRNL PMID 22786881 JRNL DOI 10.1182/BLOOD-2012-03-419598 REMARK 2 REMARK 2 RESOLUTION. 2.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0072 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) : 2.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 66.52 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 84.0 REMARK 3 NUMBER OF REFLECTIONS : 29436 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) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1573 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) : 2.09 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.14 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2239 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.43 REMARK 3 BIN R VALUE (WORKING SET) : 0.3170 REMARK 3 BIN FREE R VALUE SET COUNT : 118 REMARK 3 BIN FREE R VALUE : 0.3240 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3083 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 18 REMARK 3 SOLVENT ATOMS : 27 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.83 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.35000 REMARK 3 B22 (A**2) : -0.49000 REMARK 3 B33 (A**2) : 0.17000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.34000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.202 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.182 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.109 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.127 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.930 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3160 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2233 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4256 ; 1.541 ; 1.979 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5428 ; 0.862 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 379 ; 6.919 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 139 ;30.460 ;23.309 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 592 ;15.878 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;22.375 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 471 ; 0.087 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3408 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 659 ; 0.001 ; 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): 1899 ; 0.883 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 768 ; 0.185 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3075 ; 1.658 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1261 ; 2.406 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1181 ; 3.971 ; 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 : 2 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 : A 40 A 386 REMARK 3 ORIGIN FOR THE GROUP (A): 6.4048 -17.2980 27.4469 REMARK 3 T TENSOR REMARK 3 T11: 0.0248 T22: 0.0446 REMARK 3 T33: 0.0331 T12: 0.0037 REMARK 3 T13: 0.0060 T23: -0.0260 REMARK 3 L TENSOR REMARK 3 L11: 1.5788 L22: 1.2909 REMARK 3 L33: 1.1625 L12: 0.7292 REMARK 3 L13: -0.3507 L23: -0.5204 REMARK 3 S TENSOR REMARK 3 S11: -0.0059 S12: 0.0097 S13: 0.0332 REMARK 3 S21: -0.0222 S22: -0.0050 S23: 0.0441 REMARK 3 S31: -0.0728 S32: 0.0508 S33: 0.0110 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 : B 390 B 423 REMARK 3 ORIGIN FOR THE GROUP (A): 15.3097 -6.4488 22.0197 REMARK 3 T TENSOR REMARK 3 T11: 0.0315 T22: 0.0273 REMARK 3 T33: 0.0356 T12: -0.0241 REMARK 3 T13: 0.0014 T23: 0.0029 REMARK 3 L TENSOR REMARK 3 L11: 0.7983 L22: 2.3058 REMARK 3 L33: 2.4884 L12: -0.0141 REMARK 3 L13: -0.0761 L23: -1.4174 REMARK 3 S TENSOR REMARK 3 S11: -0.0494 S12: 0.0548 S13: 0.0778 REMARK 3 S21: -0.1182 S22: -0.0231 S23: -0.1470 REMARK 3 S31: -0.0483 S32: 0.1144 S33: 0.0725 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 4AFX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-JAN-12. REMARK 100 THE DEPOSITION ID IS D_1290051016. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31054 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.090 REMARK 200 RESOLUTION RANGE LOW (A) : 44.390 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 84.3 REMARK 200 DATA REDUNDANCY : 87.00 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.09 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.47000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 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: PDB ENTRY 7API REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8M NAK PHOSPHATE, PH5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z+1/2 REMARK 290 4555 -X+1/2,Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 23.84280 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 53.33000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.47070 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 23.84280 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 53.33000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 37.47070 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -81.1 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 ENGINEERED RESIDUE IN CHAIN A, TYR 408 TO ARG REMARK 400 ENGINEERED RESIDUE IN CHAIN B, TYR 408 TO ARG 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 SER A 1 REMARK 465 ALA A 2 REMARK 465 PRO A 3 REMARK 465 SER A 4 REMARK 465 PRO A 5 REMARK 465 GLN A 6 REMARK 465 SER A 7 REMARK 465 PRO A 8 REMARK 465 GLU A 9 REMARK 465 THR A 10 REMARK 465 PRO A 11 REMARK 465 ALA A 12 REMARK 465 PRO A 13 REMARK 465 GLN A 14 REMARK 465 ASN A 15 REMARK 465 GLN A 16 REMARK 465 THR A 17 REMARK 465 SER A 18 REMARK 465 ARG A 19 REMARK 465 VAL A 20 REMARK 465 VAL A 21 REMARK 465 GLN A 22 REMARK 465 ALA A 23 REMARK 465 PRO A 24 REMARK 465 LYS A 25 REMARK 465 GLU A 26 REMARK 465 GLU A 27 REMARK 465 GLU A 28 REMARK 465 GLU A 29 REMARK 465 ASP A 30 REMARK 465 GLU A 31 REMARK 465 GLN A 32 REMARK 465 GLU A 33 REMARK 465 ALA A 34 REMARK 465 SER A 35 REMARK 465 GLU A 36 REMARK 465 GLU A 37 REMARK 465 LYS A 38 REMARK 465 ALA A 39 REMARK 465 ARG A 387 REMARK 465 SER B 388 REMARK 465 MET B 389 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 GLU A 57 CD OE1 OE2 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 GLU A 57 CG GLU A 57 CD 0.126 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 ARG A 338 NE - CZ - NH2 ANGL. DEV. = -4.1 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 ASP A 201 -82.23 -120.18 REMARK 500 HIS A 288 -176.65 -61.20 REMARK 500 THR A 352 -94.03 -89.66 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 THR A 352 GLY A 353 -146.82 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 NA A 1387 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1388 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 1389 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 1390 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1391 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 1392 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4AJU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE REACTIVE LOOP CLEAVED ZPI IN P41 SPACE REMARK 900 GROUP DBREF 4AFX A 2 387 UNP Q9UK55 ZPI_HUMAN 23 408 DBREF 4AFX B 388 423 UNP Q9UK55 ZPI_HUMAN 409 444 SEQADV 4AFX SER A 1 UNP Q9UK55 EXPRESSION TAG SEQADV 4AFX ARG A 387 UNP Q9UK55 TYR 408 ENGINEERED MUTATION SEQADV 4AFX ILE B 395 UNP Q9UK55 VAL 416 CONFLICT SEQRES 1 A 387 SER ALA PRO SER PRO GLN SER PRO GLU THR PRO ALA PRO SEQRES 2 A 387 GLN ASN GLN THR SER ARG VAL VAL GLN ALA PRO LYS GLU SEQRES 3 A 387 GLU GLU GLU ASP GLU GLN GLU ALA SER GLU GLU LYS ALA SEQRES 4 A 387 SER GLU GLU GLU LYS ALA TRP LEU MET ALA SER ARG GLN SEQRES 5 A 387 GLN LEU ALA LYS GLU THR SER ASN PHE GLY PHE SER LEU SEQRES 6 A 387 LEU ARG LYS ILE SER MET ARG HIS ASP GLY ASN MET VAL SEQRES 7 A 387 PHE SER PRO PHE GLY MET SER LEU ALA MET THR GLY LEU SEQRES 8 A 387 MET LEU GLY ALA THR GLY PRO THR GLU THR GLN ILE LYS SEQRES 9 A 387 ARG GLY LEU HIS LEU GLN ALA LEU LYS PRO THR LYS PRO SEQRES 10 A 387 GLY LEU LEU PRO SER LEU PHE LYS GLY LEU ARG GLU THR SEQRES 11 A 387 LEU SER ARG ASN LEU GLU LEU GLY LEU THR GLN GLY SER SEQRES 12 A 387 PHE ALA PHE ILE HIS LYS ASP PHE ASP VAL LYS GLU THR SEQRES 13 A 387 PHE PHE ASN LEU SER LYS ARG TYR PHE ASP THR GLU CYS SEQRES 14 A 387 VAL PRO MET ASN PHE ARG ASN ALA SER GLN ALA LYS ARG SEQRES 15 A 387 LEU MET ASN HIS TYR ILE ASN LYS GLU THR ARG GLY LYS SEQRES 16 A 387 ILE PRO LYS LEU PHE ASP GLU ILE ASN PRO GLU THR LYS SEQRES 17 A 387 LEU ILE LEU VAL ASP TYR ILE LEU PHE LYS GLY LYS TRP SEQRES 18 A 387 LEU THR PRO PHE ASP PRO VAL PHE THR GLU VAL ASP THR SEQRES 19 A 387 PHE HIS LEU ASP LYS TYR LYS THR ILE LYS VAL PRO MET SEQRES 20 A 387 MET TYR GLY ALA GLY LYS PHE ALA SER THR PHE ASP LYS SEQRES 21 A 387 ASN PHE ARG CYS HIS VAL LEU LYS LEU PRO TYR GLN GLY SEQRES 22 A 387 ASN ALA THR MET LEU VAL VAL LEU MET GLU LYS MET GLY SEQRES 23 A 387 ASP HIS LEU ALA LEU GLU ASP TYR LEU THR THR ASP LEU SEQRES 24 A 387 VAL GLU THR TRP LEU ARG ASN MET LYS THR ARG ASN MET SEQRES 25 A 387 GLU VAL PHE PHE PRO LYS PHE LYS LEU ASP GLN LYS TYR SEQRES 26 A 387 GLU MET HIS GLU LEU LEU ARG GLN MET GLY ILE ARG ARG SEQRES 27 A 387 ILE PHE SER PRO PHE ALA ASP LEU SER GLU LEU SER ALA SEQRES 28 A 387 THR GLY ARG ASN LEU GLN VAL SER ARG VAL LEU GLN ARG SEQRES 29 A 387 THR VAL ILE GLU VAL ASP GLU ARG GLY THR GLU ALA VAL SEQRES 30 A 387 ALA GLY ILE LEU SER GLU ILE THR ALA ARG SEQRES 1 B 36 SER MET PRO PRO VAL ILE LYS ILE ASP ARG PRO PHE HIS SEQRES 2 B 36 PHE MET ILE TYR GLU GLU THR SER GLY MET LEU LEU PHE SEQRES 3 B 36 LEU GLY ARG VAL VAL ASN PRO THR LEU LEU HET NA A1387 1 HET CA A1388 1 HET PO4 A1389 5 HET PO4 A1390 5 HET NA A1391 1 HET PO4 A1392 5 HETNAM NA SODIUM ION HETNAM CA CALCIUM ION HETNAM PO4 PHOSPHATE ION FORMUL 3 NA 2(NA 1+) FORMUL 4 CA CA 2+ FORMUL 5 PO4 3(O4 P 3-) FORMUL 9 HOH *27(H2 O) HELIX 1 1 SER A 40 HIS A 73 1 34 HELIX 2 2 SER A 80 LEU A 93 1 14 HELIX 3 3 GLY A 97 LEU A 107 1 11 HELIX 4 4 GLY A 118 ASN A 134 1 17 HELIX 5 5 LEU A 135 LEU A 137 5 3 HELIX 6 6 LYS A 154 ASP A 166 1 13 HELIX 7 7 ASN A 176 THR A 192 1 17 HELIX 8 8 ASP A 226 THR A 230 5 5 HELIX 9 9 ALA A 290 TYR A 294 5 5 HELIX 10 10 THR A 296 ASN A 306 1 11 HELIX 11 11 MET A 327 MET A 334 1 8 HELIX 12 12 ARG A 337 SER A 341 5 5 SHEET 1 AA 8 MET A 77 PHE A 79 0 SHEET 2 AA 8 MET B 410 VAL B 417 -1 O LEU B 414 N PHE A 79 SHEET 3 AA 8 PHE B 399 GLU B 405 -1 O PHE B 399 N VAL B 417 SHEET 4 AA 8 ALA A 275 MET A 282 -1 O THR A 276 N TYR B 404 SHEET 5 AA 8 CYS A 264 PRO A 270 -1 O HIS A 265 N LEU A 281 SHEET 6 AA 8 THR A 242 ASP A 259 -1 O ALA A 255 N LYS A 268 SHEET 7 AA 8 LYS A 308 PRO A 317 1 O LYS A 308 N SER A 256 SHEET 8 AA 8 VAL B 392 LYS B 394 -1 O ILE B 393 N PHE A 315 SHEET 1 AB 7 MET A 77 PHE A 79 0 SHEET 2 AB 7 MET B 410 VAL B 417 -1 O LEU B 414 N PHE A 79 SHEET 3 AB 7 PHE B 399 GLU B 405 -1 O PHE B 399 N VAL B 417 SHEET 4 AB 7 ALA A 275 MET A 282 -1 O THR A 276 N TYR B 404 SHEET 5 AB 7 CYS A 264 PRO A 270 -1 O HIS A 265 N LEU A 281 SHEET 6 AB 7 THR A 242 ASP A 259 -1 O ALA A 255 N LYS A 268 SHEET 7 AB 7 GLU A 231 HIS A 236 -1 O GLU A 231 N MET A 247 SHEET 1 AC 6 GLU A 168 MET A 172 0 SHEET 2 AC 6 LEU A 139 HIS A 148 1 O SER A 143 N GLU A 168 SHEET 3 AC 6 THR A 207 LYS A 220 -1 O LYS A 208 N HIS A 148 SHEET 4 AC 6 GLY A 373 THR A 385 -1 O THR A 374 N GLY A 219 SHEET 5 AC 6 GLN A 357 VAL A 369 -1 O GLN A 357 N THR A 385 SHEET 6 AC 6 PHE A 319 GLU A 326 -1 O PHE A 319 N VAL A 369 LINK OE1 GLU A 292 NA NA A1387 1555 1555 2.86 SITE 1 AC1 1 GLU A 292 SITE 1 AC2 2 ASN A 159 ARG A 163 SITE 1 AC3 2 SER A 64 ARG A 67 SITE 1 AC4 6 GLU A 100 LYS A 104 PRO A 117 GLY A 118 SITE 2 AC4 6 LEU A 120 PRO A 121 SITE 1 AC5 1 GLN A 102 SITE 1 AC6 4 HIS A 73 GLY A 75 ASN A 76 GLN A 323 CRYST1 78.850 106.660 81.163 90.00 112.58 90.00 I 1 2 1 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 0.012682 0.000000 0.005274 0.00000 SCALE2 0.000000 0.009376 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013344 0.00000