HEADER HYDROLASE 18-MAR-09 3GO9 TITLE PREDICTED INSULINASE FAMILY PROTEASE FROM YERSINIA PESTIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: INSULINASE FAMILY PROTEASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: YERSINIA PESTIS; SOURCE 3 ORGANISM_TAXID: 632; SOURCE 4 STRAIN: CO92; SOURCE 5 GENE: PQQL, Y3837, YPO3991, YP_3354; 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 EXPRESSION_SYSTEM_PLASMID: PMCSG7 KEYWDS IDP00573, INSULINASE FAMILY, PROTEASE, STRUCTURAL GENOMICS, CENTER KEYWDS 2 FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES, CSGID, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.OSIPIUK,N.MALTSEVA,O.ONOPRIYENKO,S.PETERSON,W.F.ANDERSON, AUTHOR 2 A.JOACHIMIAK,CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES AUTHOR 3 (CSGID) REVDAT 3 01-NOV-17 3GO9 1 REMARK REVDAT 2 13-JUL-11 3GO9 1 VERSN REVDAT 1 07-APR-09 3GO9 0 JRNL AUTH J.OSIPIUK,N.MALTSEVA,O.ONOPRIYENKO,S.PETERSON,W.F.ANDERSON, JRNL AUTH 2 A.JOACHIMIAK JRNL TITL X-RAY CRYSTAL STRUCTURE OF PREDICTED INSULINASE FAMILY JRNL TITL 2 PROTEASE FROM YERSINIA PESTIS. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.62 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0054 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.62 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 56662 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) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2871 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) : 1.62 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.66 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3865 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.46 REMARK 3 BIN R VALUE (WORKING SET) : 0.2460 REMARK 3 BIN FREE R VALUE SET COUNT : 191 REMARK 3 BIN FREE R VALUE : 0.3120 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3609 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 493 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 27.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.64000 REMARK 3 B22 (A**2) : 0.38000 REMARK 3 B33 (A**2) : 0.28000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.06000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.093 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.094 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.062 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.726 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.955 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3830 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2610 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5240 ; 1.693 ; 1.966 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6416 ; 0.953 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 498 ; 5.784 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 183 ;38.637 ;25.082 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 674 ;14.003 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;16.701 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 589 ; 0.100 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4284 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 722 ; 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): 2361 ; 1.045 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 926 ; 0.332 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3833 ; 1.817 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1469 ; 2.896 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1386 ; 4.514 ; 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 : 1 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 -2 A 499 REMARK 3 ORIGIN FOR THE GROUP (A): 8.5536 14.4269 25.4818 REMARK 3 T TENSOR REMARK 3 T11: 0.0215 T22: 0.0211 REMARK 3 T33: 0.0370 T12: 0.0066 REMARK 3 T13: -0.0086 T23: 0.0151 REMARK 3 L TENSOR REMARK 3 L11: 0.2984 L22: 0.1182 REMARK 3 L33: 0.4302 L12: 0.0581 REMARK 3 L13: -0.1291 L23: 0.1050 REMARK 3 S TENSOR REMARK 3 S11: 0.0060 S12: 0.0539 S13: 0.0069 REMARK 3 S21: -0.0052 S22: -0.0055 S23: 0.0009 REMARK 3 S31: 0.0084 S32: -0.0213 S33: -0.0005 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 3GO9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000052108. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAR-09 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 : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-3000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 56782 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.620 REMARK 200 RESOLUTION RANGE LOW (A) : 42.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 32.2330 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.62 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.76900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.810 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXD, MLPHARE, DM, SOLVE, RESOLVE, HKL-3000 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.02 M ZINC CHLORIDE, 0.1 M YTRIUM REMARK 280 CHLORIDE, 20% PEG-3350, PH 7.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 40.11500 REMARK 290 SMTRY3 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 LEU A 15 REMARK 465 ALA A 16 REMARK 465 ALA A 17 REMARK 465 ALA A 18 REMARK 465 SER A 19 REMARK 465 ASN A 20 REMARK 465 ASN A 21 REMARK 465 VAL A 22 REMARK 465 PRO A 474 REMARK 465 GLN A 475 REMARK 465 THR A 476 REMARK 465 VAL A 477 REMARK 465 ALA A 478 REMARK 465 GLU A 479 REMARK 465 GLU A 480 REMARK 465 GLU A 481 REMARK 465 VAL A 482 REMARK 465 ALA A 483 REMARK 465 PRO A 484 REMARK 465 ALA A 485 REMARK 465 GLU A 486 REMARK 465 ALA A 487 REMARK 465 VAL A 488 REMARK 465 GLU A 489 REMARK 465 THR A 490 REMARK 465 ALA A 491 REMARK 465 PRO A 492 REMARK 465 VAL A 493 REMARK 465 MSE A 494 REMARK 465 PRO A 495 REMARK 465 THR A 496 REMARK 465 THR A 497 REMARK 465 ALA A 498 REMARK 465 GLN A 499 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 ZN ZN A 602 O HOH A 534 1.64 REMARK 500 O HOH A 735 O HOH A 843 2.18 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 CYS A 337 CB CYS A 337 SG 0.310 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 ASP A 133 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ASP A 192 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG A 247 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 ARG A 247 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 MSE A 267 CG - SE - CE ANGL. DEV. = 15.0 DEGREES REMARK 500 CYS A 337 CB - CA - C ANGL. DEV. = 11.8 DEGREES REMARK 500 CYS A 337 CA - CB - SG ANGL. DEV. = 8.9 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 ARG A 52 64.82 -119.78 REMARK 500 ASN A 148 41.15 -142.59 REMARK 500 REMARK 500 REMARK: NULL 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 ZN A 602 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 79 NE2 REMARK 620 2 ASP A 165 OD2 150.6 REMARK 620 3 ILE A 167 O 97.3 88.9 REMARK 620 4 HOH A 795 O 110.3 98.8 86.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 601 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 106 OD2 REMARK 620 2 GLU A 108 OE1 91.7 REMARK 620 3 HOH A 3 O 79.9 158.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 603 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 309 NE2 REMARK 620 2 GLU A 358 OE1 101.7 REMARK 620 3 HOH A 658 O 110.1 108.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 604 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 327 OD1 REMARK 620 2 ASP A 327 OD2 59.0 REMARK 620 3 HIS A 340 NE2 118.4 98.5 REMARK 620 4 HOH A 523 O 91.7 146.7 110.2 REMARK 620 5 HOH A 869 O 125.2 82.7 103.7 105.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 605 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 416 OE1 REMARK 620 2 HOH A 841 O 83.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 606 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 943 O REMARK 620 2 HOH A 942 O 72.6 REMARK 620 3 HOH A 857 O 71.1 140.5 REMARK 620 4 HOH A 984 O 140.1 145.1 68.9 REMARK 620 5 HOH A 944 O 123.7 93.7 119.4 77.3 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 607 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: IDP00573 RELATED DB: TARGETDB DBREF 3GO9 A 8 499 UNP Q7CG15 Q7CG15_YERPE 8 499 SEQRES 1 A 492 LEU MSE VAL GLY GLY LEU LEU LEU ALA ALA ALA SER ASN SEQRES 2 A 492 ASN VAL GLN ALA GLU ALA LEU GLN PRO ASP PRO ALA TRP SEQRES 3 A 492 GLN GLN GLY LYS LEU ASP ASN GLY PHE SER TRP GLN LEU SEQRES 4 A 492 LEU ALA THR PRO GLN ARG PRO SER ASP ARG ILE GLU LEU SEQRES 5 A 492 ARG LEU ILE VAL ASN THR GLY SER LEU SER GLU ASN THR SEQRES 6 A 492 GLN GLU VAL GLY PHE ALA HIS LEU LEU PRO ARG LEU ALA SEQRES 7 A 492 LEU MSE SER SER ALA SER PHE THR PRO ALA GLN LEU GLN SEQRES 8 A 492 SER LEU TRP GLN GLN GLY ILE ASP ASN GLU ARG PRO LEU SEQRES 9 A 492 PRO PRO ALA ILE THR SER TYR ASP PHE THR LEU TYR SER SEQRES 10 A 492 LEU SER LEU PRO ASN ASN ARG PRO ASP LEU LEU LYS ASP SEQRES 11 A 492 ALA LEU ALA TRP LEU SER ASP THR ALA GLY ASN LEU ALA SEQRES 12 A 492 VAL SER GLU GLN THR VAL ASN ALA ALA LEU ASN THR ALA SEQRES 13 A 492 THR ASP PRO ILE ALA THR PHE PRO GLN ASN ILE GLN GLU SEQRES 14 A 492 PRO TRP TRP ARG TYR ARG LEU LYS GLY SER SER LEU ILE SEQRES 15 A 492 GLY HIS ASP PRO GLY GLN PRO VAL THR GLN PRO VAL ASP SEQRES 16 A 492 VAL GLU LYS LEU LYS GLN PHE TYR GLN GLN TRP TYR THR SEQRES 17 A 492 PRO ASP ALA MSE THR LEU TYR VAL VAL GLY ASN VAL ASP SEQRES 18 A 492 SER ARG SER ILE ALA ALA GLN ILE SER LYS ALA PHE SER SEQRES 19 A 492 GLU LEU LYS GLY LYS ARG THR ALA PRO ALA ALA VAL ALA SEQRES 20 A 492 THR LEU ALA PRO LEU PRO PRO GLU PRO VAL SER LEU MSE SEQRES 21 A 492 ASN GLU GLN ALA ALA GLN ASP THR LEU SER LEU MSE TRP SEQRES 22 A 492 ASP THR PRO TRP HIS PRO ILE GLN ASP SER MSE ALA LEU SEQRES 23 A 492 SER ARG TYR TRP ARG SER ASP LEU ALA ARG GLU ALA LEU SEQRES 24 A 492 PHE TRP HIS ILE LYS GLN VAL LEU GLU LYS ASN ASN GLN SEQRES 25 A 492 LYS ASN LEU LYS LEU GLY PHE ASP CYS ARG VAL GLN TYR SEQRES 26 A 492 GLN ARG ALA GLN CYS ALA ILE HIS LEU ASN THR PRO VAL SEQRES 27 A 492 GLU ASN LEU THR ALA ASN MSE THR PHE VAL ALA ARG GLU SEQRES 28 A 492 LEU ALA ALA LEU ARG ALA ASN GLY LEU SER GLN ALA GLU SEQRES 29 A 492 PHE ASP ALA LEU MSE THR GLN LYS ASN ASP GLN LEU SER SEQRES 30 A 492 LYS LEU PHE ALA THR TYR ALA ARG THR ASP THR ASP ILE SEQRES 31 A 492 LEU MSE SER GLN ARG LEU ARG SER GLN GLN SER GLY VAL SEQRES 32 A 492 VAL ASP ILE ALA PRO GLU GLN TYR GLN LYS LEU ARG GLN SEQRES 33 A 492 ALA PHE LEU SER GLY LEU THR LEU ALA GLU LEU ASN ARG SEQRES 34 A 492 GLU LEU LYS GLN GLN LEU SER GLN ASP THR THR LEU VAL SEQRES 35 A 492 LEU MSE GLN PRO LYS GLY GLU PRO GLU VAL ASN VAL LYS SEQRES 36 A 492 ALA LEU GLN GLU ILE TYR ASN GLY ILE MSE ALA PRO GLN SEQRES 37 A 492 THR VAL ALA GLU GLU GLU VAL ALA PRO ALA GLU ALA VAL SEQRES 38 A 492 GLU THR ALA PRO VAL MSE PRO THR THR ALA GLN MODRES 3GO9 MSE A 9 MET SELENOMETHIONINE MODRES 3GO9 MSE A 87 MET SELENOMETHIONINE MODRES 3GO9 MSE A 219 MET SELENOMETHIONINE MODRES 3GO9 MSE A 267 MET SELENOMETHIONINE MODRES 3GO9 MSE A 279 MET SELENOMETHIONINE MODRES 3GO9 MSE A 291 MET SELENOMETHIONINE MODRES 3GO9 MSE A 352 MET SELENOMETHIONINE MODRES 3GO9 MSE A 376 MET SELENOMETHIONINE MODRES 3GO9 MSE A 399 MET SELENOMETHIONINE MODRES 3GO9 MSE A 451 MET SELENOMETHIONINE MODRES 3GO9 MSE A 472 MET SELENOMETHIONINE HET MSE A 9 8 HET MSE A 87 8 HET MSE A 219 8 HET MSE A 267 13 HET MSE A 279 13 HET MSE A 291 13 HET MSE A 352 8 HET MSE A 376 13 HET MSE A 399 8 HET MSE A 451 8 HET MSE A 472 8 HET ZN A 601 1 HET ZN A 602 1 HET ZN A 603 1 HET ZN A 604 1 HET ZN A 605 1 HET ZN A 606 1 HET PEG A 607 7 HETNAM MSE SELENOMETHIONINE HETNAM ZN ZINC ION HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 1 MSE 11(C5 H11 N O2 SE) FORMUL 2 ZN 6(ZN 2+) FORMUL 8 PEG C4 H10 O3 FORMUL 9 HOH *493(H2 O) HELIX 1 1 GLY A 66 GLU A 70 5 5 HELIX 2 2 ASN A 71 VAL A 75 5 5 HELIX 3 3 GLY A 76 SER A 88 1 13 HELIX 4 4 THR A 93 GLN A 103 1 11 HELIX 5 5 ARG A 131 ASN A 148 1 18 HELIX 6 6 SER A 152 ASN A 161 1 10 HELIX 7 7 GLU A 176 LEU A 183 1 8 HELIX 8 8 ASP A 202 TYR A 214 1 13 HELIX 9 9 THR A 215 ASP A 217 5 3 HELIX 10 10 ASP A 228 SER A 241 1 14 HELIX 11 11 ASP A 289 ASN A 317 1 29 HELIX 12 12 PRO A 344 GLU A 346 5 3 HELIX 13 13 ASN A 347 GLY A 366 1 20 HELIX 14 14 SER A 368 LYS A 385 1 18 HELIX 15 15 LYS A 385 ARG A 392 1 8 HELIX 16 16 ASP A 394 GLY A 409 1 16 HELIX 17 17 ALA A 414 LEU A 429 1 16 HELIX 18 18 THR A 430 SER A 443 1 14 HELIX 19 19 ASN A 460 ALA A 473 1 14 SHEET 1 A 7 TRP A 33 LYS A 37 0 SHEET 2 A 7 SER A 43 ALA A 48 -1 O LEU A 46 N GLN A 34 SHEET 3 A 7 MSE A 219 GLY A 225 1 O VAL A 223 N LEU A 47 SHEET 4 A 7 ILE A 57 VAL A 63 -1 N ARG A 60 O TYR A 222 SHEET 5 A 7 THR A 121 LEU A 127 -1 O LEU A 127 N ILE A 57 SHEET 6 A 7 ALA A 114 THR A 116 -1 N ILE A 115 O LEU A 122 SHEET 7 A 7 ILE A 167 THR A 169 1 O ALA A 168 N THR A 116 SHEET 1 B 5 VAL A 264 ASN A 268 0 SHEET 2 B 5 THR A 447 PRO A 453 1 O GLN A 452 N ASN A 268 SHEET 3 B 5 ASP A 274 PRO A 283 -1 N SER A 277 O VAL A 449 SHEET 4 B 5 ARG A 334 THR A 343 -1 O ALA A 335 N THR A 282 SHEET 5 B 5 LYS A 323 GLN A 331 -1 N LYS A 323 O ASN A 342 SSBOND 1 CYS A 328 CYS A 337 1555 1555 2.07 LINK C LEU A 8 N MSE A 9 1555 1555 1.32 LINK C MSE A 9 N VAL A 10 1555 1555 1.32 LINK C LEU A 86 N MSE A 87 1555 1555 1.33 LINK C MSE A 87 N SER A 88 1555 1555 1.32 LINK C ALA A 218 N MSE A 219 1555 1555 1.33 LINK C MSE A 219 N THR A 220 1555 1555 1.32 LINK C LEU A 266 N MSE A 267 1555 1555 1.35 LINK C MSE A 267 N ASN A 268 1555 1555 1.32 LINK C LEU A 278 N MSE A 279 1555 1555 1.34 LINK C MSE A 279 N TRP A 280 1555 1555 1.32 LINK C SER A 290 N MSE A 291 1555 1555 1.33 LINK C MSE A 291 N ALA A 292 1555 1555 1.33 LINK C ASN A 351 N MSE A 352 1555 1555 1.33 LINK C MSE A 352 N THR A 353 1555 1555 1.33 LINK C LEU A 375 N MSE A 376 1555 1555 1.33 LINK C MSE A 376 N THR A 377 1555 1555 1.34 LINK C LEU A 398 N MSE A 399 1555 1555 1.33 LINK C MSE A 399 N SER A 400 1555 1555 1.35 LINK C LEU A 450 N MSE A 451 1555 1555 1.33 LINK C MSE A 451 N GLN A 452 1555 1555 1.32 LINK C ILE A 471 N MSE A 472 1555 1555 1.32 LINK C MSE A 472 N ALA A 473 1555 1555 1.33 LINK NE2 HIS A 79 ZN ZN A 602 1555 1555 2.02 LINK OD2 ASP A 106 ZN ZN A 601 1555 1555 2.32 LINK OE1 GLU A 108 ZN ZN A 601 1555 1555 2.24 LINK OD2 ASP A 165 ZN ZN A 602 1555 1555 1.91 LINK O ILE A 167 ZN ZN A 602 1555 1555 2.37 LINK NE2 HIS A 309 ZN ZN A 603 1555 1555 2.03 LINK OD1 ASP A 327 ZN ZN A 604 1555 1555 2.36 LINK OD2 ASP A 327 ZN ZN A 604 1555 1555 1.94 LINK NE2 HIS A 340 ZN ZN A 604 1555 1555 2.14 LINK OE1 GLU A 358 ZN ZN A 603 1555 1555 1.99 LINK OE1 GLU A 416 ZN ZN A 605 1555 1555 2.14 LINK ZN ZN A 601 O HOH A 3 1555 1555 2.35 LINK ZN ZN A 602 O HOH A 795 1555 1555 1.89 LINK ZN ZN A 603 O HOH A 658 1555 1555 1.99 LINK ZN ZN A 604 O HOH A 523 1555 1555 2.08 LINK ZN ZN A 604 O HOH A 869 1555 1555 2.10 LINK ZN ZN A 605 O HOH A 841 1555 1555 1.83 LINK ZN ZN A 606 O HOH A 943 1555 1555 2.38 LINK ZN ZN A 606 O HOH A 942 1555 1555 1.99 LINK ZN ZN A 606 O HOH A 857 1555 1555 2.39 LINK ZN ZN A 606 O HOH A 984 1555 1555 2.04 LINK ZN ZN A 606 O HOH A 944 1555 1555 2.18 CISPEP 1 PHE A 170 PRO A 171 0 -9.96 CISPEP 2 GLN A 199 PRO A 200 0 -2.84 SITE 1 AC1 6 HOH A 3 ASP A 106 GLU A 108 ASP A 394 SITE 2 AC1 6 ASP A 396 HOH A 521 SITE 1 AC2 5 HIS A 79 ASP A 165 ILE A 167 HOH A 534 SITE 2 AC2 5 HOH A 795 SITE 1 AC3 5 GLU A 242 HIS A 309 VAL A 313 GLU A 358 SITE 2 AC3 5 HOH A 658 SITE 1 AC4 4 ASP A 327 HIS A 340 HOH A 523 HOH A 869 SITE 1 AC5 2 GLU A 416 HOH A 841 SITE 1 AC6 5 HOH A 857 HOH A 942 HOH A 943 HOH A 944 SITE 2 AC6 5 HOH A 984 SITE 1 AC7 8 LEU A 13 LEU A 14 TYR A 296 ASP A 300 SITE 2 AC7 8 ARG A 303 CYS A 328 ARG A 329 CYS A 337 CRYST1 42.890 80.230 66.620 90.00 99.34 90.00 P 1 21 1 2 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 0.023315 0.000000 0.003836 0.00000 SCALE2 0.000000 0.012464 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015212 0.00000