HEADER HYDROLASE 08-JUN-16 5KDN TITLE ZMPB METALLOPEPTIDASE FROM CLOSTRIDIUM PERFRINGENS COMPND MOL_ID: 1; COMPND 2 MOLECULE: F5/8 TYPE C DOMAIN PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 497-1003; COMPND 5 SYNONYM: METALLOPEPTIDASE; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM PERFRINGENS (STRAIN ATCC 13124 / SOURCE 3 DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / TYPE A); SOURCE 4 ORGANISM_TAXID: 195103; SOURCE 5 STRAIN: ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / SOURCE 6 TYPE A; SOURCE 7 GENE: CPF_1489; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS O-GLYCOPEPTIDASE, PF13402/M60-LIKE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR I.NOACH,E.FICKO-BLEAN,C.STUART,A.B.BORASTON REVDAT 4 27-SEP-23 5KDN 1 LINK REVDAT 3 08-FEB-17 5KDN 1 JRNL REVDAT 2 01-FEB-17 5KDN 1 JRNL REVDAT 1 11-JAN-17 5KDN 0 JRNL AUTH I.NOACH,E.FICKO-BLEAN,B.PLUVINAGE,C.STUART,M.L.JENKINS, JRNL AUTH 2 D.BROCHU,N.BUENBRAZO,W.WAKARCHUK,J.E.BURKE,M.GILBERT, JRNL AUTH 3 A.B.BORASTON JRNL TITL RECOGNITION OF PROTEIN-LINKED GLYCANS AS A DETERMINANT OF JRNL TITL 2 PEPTIDASE ACTIVITY. JRNL REF PROC. NATL. ACAD. SCI. V. 114 E679 2017 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 28096352 JRNL DOI 10.1073/PNAS.1615141114 REMARK 2 REMARK 2 RESOLUTION. 1.66 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 1.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.09 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 87452 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) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4594 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) : 1.66 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.70 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6391 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.99 REMARK 3 BIN R VALUE (WORKING SET) : 0.1940 REMARK 3 BIN FREE R VALUE SET COUNT : 351 REMARK 3 BIN FREE R VALUE : 0.2250 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4063 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 21 REMARK 3 SOLVENT ATOMS : 622 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.36000 REMARK 3 B22 (A**2) : 2.90000 REMARK 3 B33 (A**2) : -1.54000 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): 0.069 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.071 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.048 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.412 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.963 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4312 ; 0.018 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 4003 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5840 ; 1.863 ; 1.945 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9247 ; 0.898 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 535 ; 6.402 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 219 ;38.886 ;25.205 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 749 ;13.113 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;20.301 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 608 ; 0.118 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5024 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1021 ; 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): 2101 ; 1.780 ; 2.001 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2100 ; 1.776 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2649 ; 2.612 ; 2.998 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2650 ; 2.613 ; 2.999 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2211 ; 3.020 ; 2.275 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2211 ; 3.017 ; 2.275 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3192 ; 4.569 ; 3.276 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5597 ; 6.282 ;17.925 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5598 ; 6.281 ;17.928 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 : NULL 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 5KDN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1000222066. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAY-15 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 : CLSI REMARK 200 BEAMLINE : 08B1-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97950 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 92133 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.660 REMARK 200 RESOLUTION RANGE LOW (A) : 43.090 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.66 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 0.24900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 5KDJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, NA/K TARTRATE, HEPES PH 7.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 32.94500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 85.43000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.01000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 85.43000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.94500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.01000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: 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 MET A 474 REMARK 465 GLY A 475 REMARK 465 SER A 476 REMARK 465 SER A 477 REMARK 465 HIS A 478 REMARK 465 HIS A 479 REMARK 465 HIS A 480 REMARK 465 HIS A 481 REMARK 465 HIS A 482 REMARK 465 HIS A 483 REMARK 465 SER A 484 REMARK 465 SER A 485 REMARK 465 GLY A 486 REMARK 465 LEU A 487 REMARK 465 VAL A 488 REMARK 465 PRO A 489 REMARK 465 ARG A 490 REMARK 465 GLY A 491 REMARK 465 SER A 492 REMARK 465 HIS A 493 REMARK 465 MET A 494 REMARK 465 ALA A 495 REMARK 465 ASN A 1003 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 HOH A 1437 O HOH A 1688 1.57 REMARK 500 O HOH A 1617 O HOH A 1743 1.89 REMARK 500 O HOH A 1679 O HOH A 1772 2.03 REMARK 500 O HOH A 1558 O HOH A 1727 2.06 REMARK 500 O HOH A 1453 O HOH A 1549 2.10 REMARK 500 O HOH A 1208 O HOH A 1389 2.12 REMARK 500 O HOH A 1514 O HOH A 1589 2.13 REMARK 500 O HOH A 1719 O HOH A 1734 2.14 REMARK 500 N LYS A 917 O HOH A 1201 2.17 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 GLU A 686 CD GLU A 686 OE2 -0.067 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 529 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES REMARK 500 ASP A 603 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG A 607 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 612 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ASP A 689 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 MET A 696 CA - CB - CG ANGL. DEV. = -11.0 DEGREES REMARK 500 ASP A 743 CB - CG - OD1 ANGL. DEV. = 7.6 DEGREES REMARK 500 ASP A 793 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ASP A 876 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ASN A 935 N - CA - CB ANGL. DEV. = -12.6 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 SER A 723 -167.02 -161.86 REMARK 500 ARG A 767 26.56 -142.18 REMARK 500 VAL A 772 -68.07 -120.06 REMARK 500 ASN A 800 -56.07 -130.60 REMARK 500 ASN A 935 -114.65 42.65 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 SER A 934 ASN A 935 -146.94 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 A1822 DISTANCE = 6.66 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 ZN A1106 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 756 NE2 REMARK 620 2 HIS A 760 NE2 92.2 REMARK 620 3 GLU A 771 OE1 94.1 92.2 REMARK 620 4 HOH A1300 O 96.1 170.0 81.6 REMARK 620 5 HOH A1312 O 104.4 96.1 159.3 87.3 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 EDO A 1101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 1102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 1103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 1104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 1105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1106 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5KD2 RELATED DB: PDB REMARK 900 RELATED ID: 5KD5 RELATED DB: PDB REMARK 900 RELATED ID: 5KD8 RELATED DB: PDB REMARK 900 RELATED ID: 5KDJ RELATED DB: PDB REMARK 900 RELATED ID: 5KDS RELATED DB: PDB REMARK 900 RELATED ID: 5KDU RELATED DB: PDB REMARK 900 RELATED ID: 5KDV RELATED DB: PDB REMARK 900 RELATED ID: 5KDW RELATED DB: PDB REMARK 900 RELATED ID: 5KDX RELATED DB: PDB DBREF1 5KDN A 497 1003 UNP A0A0H2YN38_CLOP1 DBREF2 5KDN A A0A0H2YN38 497 1003 SEQADV 5KDN MET A 474 UNP A0A0H2YN3 INITIATING METHIONINE SEQADV 5KDN GLY A 475 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDN SER A 476 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDN SER A 477 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDN HIS A 478 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDN HIS A 479 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDN HIS A 480 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDN HIS A 481 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDN HIS A 482 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDN HIS A 483 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDN SER A 484 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDN SER A 485 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDN GLY A 486 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDN LEU A 487 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDN VAL A 488 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDN PRO A 489 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDN ARG A 490 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDN GLY A 491 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDN SER A 492 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDN HIS A 493 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDN MET A 494 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDN ALA A 495 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDN SER A 496 UNP A0A0H2YN3 EXPRESSION TAG SEQRES 1 A 530 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 530 LEU VAL PRO ARG GLY SER HIS MET ALA SER VAL LEU GLU SEQRES 3 A 530 LEU GLU MET ARG GLY ASP SER ILE SER GLU ALA LYS LYS SEQRES 4 A 530 ARG LYS VAL TRP ASN PHE GLN ASP TRP GLN ILE THR GLY SEQRES 5 A 530 LEU SER ALA ARG ALA GLY ASP LYS ILE THR VAL TYR VAL SEQRES 6 A 530 ASP VAL ALA GLU GLY ASP PRO THR PRO THR LEU LEU TYR SEQRES 7 A 530 LYS GLN SER LEU THR GLN HIS GLY GLY ALA THR SER PHE SEQRES 8 A 530 GLN LEU LYS PRO GLY LYS ASN GLU ILE THR ILE PRO GLU SEQRES 9 A 530 ILE ASN TYR GLU SER ASN GLY ILE PRO LYS ASP VAL ILE SEQRES 10 A 530 GLN GLY GLY ASP LEU PHE PHE THR ASN TYR LYS SER ASP SEQRES 11 A 530 SER GLN LYS ARG ALA PRO LYS VAL ARG ILE GLU GLY ALA SEQRES 12 A 530 SER LYS TYR PRO VAL PHE ILE LEU GLY LYS SER ASP GLU SEQRES 13 A 530 ASN GLU VAL MET LYS GLU LEU GLU ALA TYR VAL GLU LYS SEQRES 14 A 530 ILE LYS ALA GLU PRO LYS THR THR PRO ASN ILE PHE ALA SEQRES 15 A 530 VAL SER SER ASN LYS SER LEU GLU PHE VAL GLN ALA THR SEQRES 16 A 530 TYR ALA LEU ASP TRP TYR LYS LYS ASN ASN LYS THR PRO SEQRES 17 A 530 LYS TYR THR ALA GLU GLN TRP ASP GLN TYR ILE ALA ASP SEQRES 18 A 530 ALA MET GLY PHE TRP GLY PHE ASP ASN SER LYS ASP VAL SEQRES 19 A 530 ASN SER ASP PHE ASN PHE ARG ILE MET PRO MET VAL LYS SEQRES 20 A 530 ASN LEU SER GLY GLY ALA PHE MET ASN ALA GLY ASN GLY SEQRES 21 A 530 VAL ILE GLY ILE ARG PRO GLY ASN GLN ASP ALA ILE LEU SEQRES 22 A 530 ALA ALA ASN LYS GLY TRP GLY VAL ALA HIS GLU LEU GLY SEQRES 23 A 530 HIS ASN PHE ASP THR GLY GLY ARG THR ILE VAL GLU VAL SEQRES 24 A 530 THR ASN ASN MET MET PRO LEU PHE PHE GLU SER LYS TYR SEQRES 25 A 530 LYS THR LYS THR ARG ILE THR ASP GLN ASN ILE TRP GLU SEQRES 26 A 530 ASN ASN THR TYR PRO LYS VAL GLY LEU ASP ASP TYR SER SEQRES 27 A 530 ASN ASN GLU LEU TYR ASN LYS ALA ASP SER THR HIS LEU SEQRES 28 A 530 ALA GLN LEU ALA PRO LEU TRP GLN LEU TYR LEU TYR ASP SEQRES 29 A 530 ASN THR PHE TYR GLY LYS PHE GLU ARG GLN PHE ARG GLU SEQRES 30 A 530 ARG ASP PHE GLY ASN LYS ASN ARG GLU ASP ILE TYR LYS SEQRES 31 A 530 SER TRP VAL VAL ALA ALA SER ASP ALA MET GLU LEU ASP SEQRES 32 A 530 LEU THR GLU PHE PHE ALA ARG HIS GLY ILE ARG VAL ASP SEQRES 33 A 530 ASP LYS VAL LYS GLU ASP LEU ALA LYS TYR PRO LYS PRO SEQRES 34 A 530 ASP LYS LYS ILE TYR TYR LEU ASN ASP LEU ALA MET ASN SEQRES 35 A 530 TYR LYS GLY ASP GLY PHE THR GLU ASN ALA LYS VAL SER SEQRES 36 A 530 VAL SER THR SER GLY SER ASN GLY ASN ILE LYS LEU SER SEQRES 37 A 530 PHE SER VAL ASP ASP GLU ASN LYS ASP ASN ILE LEU GLY SEQRES 38 A 530 TYR GLU ILE ARG ARG ASP GLY LYS TYR VAL GLY PHE THR SEQRES 39 A 530 SER ASN ASP SER PHE VAL ASP THR LYS SER ASN LEU ASP SEQRES 40 A 530 GLU ASP GLY VAL TYR VAL VAL THR PRO TYR ASP ARG LYS SEQRES 41 A 530 LEU ASN THR LEU ASN PRO ILE GLU VAL ASN HET EDO A1101 4 HET EDO A1102 4 HET EDO A1103 4 HET EDO A1104 4 HET EDO A1105 4 HET ZN A1106 1 HETNAM EDO 1,2-ETHANEDIOL HETNAM ZN ZINC ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO 5(C2 H6 O2) FORMUL 7 ZN ZN 2+ FORMUL 8 HOH *622(H2 O) HELIX 1 AA1 ASP A 505 ARG A 513 1 9 HELIX 2 AA2 ASN A 579 GLY A 584 1 6 HELIX 3 AA3 LYS A 601 GLN A 605 5 5 HELIX 4 AA4 ASP A 628 GLU A 646 1 19 HELIX 5 AA5 GLN A 666 ASN A 678 1 13 HELIX 6 AA6 THR A 680 TRP A 699 1 20 HELIX 7 AA7 LYS A 705 SER A 709 5 5 HELIX 8 AA8 ASN A 741 ALA A 748 1 8 HELIX 9 AA9 GLY A 751 ASP A 763 1 13 HELIX 10 AB1 VAL A 772 ASN A 774 5 3 HELIX 11 AB2 ASN A 775 LYS A 786 1 12 HELIX 12 AB3 THR A 789 GLN A 794 1 6 HELIX 13 AB4 ASN A 795 ASN A 800 1 6 HELIX 14 AB5 ASN A 800 GLY A 806 1 7 HELIX 15 AB6 HIS A 823 GLN A 826 5 4 HELIX 16 AB7 LEU A 827 ASP A 837 1 11 HELIX 17 AB8 THR A 839 ARG A 851 1 13 HELIX 18 AB9 ASN A 857 GLU A 874 1 18 HELIX 19 AC1 LEU A 877 GLY A 885 1 9 HELIX 20 AC2 ASP A 889 ALA A 897 1 9 HELIX 21 AC3 LYS A 905 LEU A 909 5 5 HELIX 22 AC4 ASN A 910 MET A 914 5 5 HELIX 23 AC5 ASP A 946 LYS A 949 5 4 SHEET 1 AA1 4 LEU A 498 GLU A 499 0 SHEET 2 AA1 4 LYS A 610 GLU A 614 -1 O VAL A 611 N LEU A 498 SHEET 3 AA1 4 LYS A 533 ASP A 539 -1 N THR A 535 O GLU A 614 SHEET 4 AA1 4 GLY A 569 THR A 574 -1 O ILE A 573 N ILE A 534 SHEET 1 AA2 5 THR A 562 GLN A 565 0 SHEET 2 AA2 5 THR A 548 GLN A 553 -1 N TYR A 551 O THR A 562 SHEET 3 AA2 5 GLY A 593 THR A 598 -1 O PHE A 596 N LEU A 550 SHEET 4 AA2 5 GLN A 522 ALA A 528 -1 N GLN A 522 O PHE A 597 SHEET 5 AA2 5 SER A 617 LYS A 618 -1 O SER A 617 N SER A 527 SHEET 1 AA3 3 VAL A 621 ILE A 623 0 SHEET 2 AA3 3 PHE A 654 SER A 657 1 O SER A 657 N PHE A 622 SHEET 3 AA3 3 LEU A 662 VAL A 665 -1 O GLU A 663 N VAL A 656 SHEET 1 AA4 3 MET A 716 VAL A 719 0 SHEET 2 AA4 3 VAL A 734 ILE A 737 1 O ILE A 735 N MET A 718 SHEET 3 AA4 3 MET A 728 GLY A 731 -1 N ASN A 729 O GLY A 736 SHEET 1 AA5 3 VAL A 927 SER A 934 0 SHEET 2 AA5 3 ASN A 937 VAL A 944 -1 O LYS A 939 N SER A 932 SHEET 3 AA5 3 SER A 971 ASP A 974 -1 O PHE A 972 N LEU A 940 SHEET 1 AA6 4 LYS A 962 THR A 967 0 SHEET 2 AA6 4 ILE A 952 ARG A 959 -1 N ILE A 957 O GLY A 965 SHEET 3 AA6 4 TYR A 985 ASP A 991 -1 O TYR A 990 N LEU A 953 SHEET 4 AA6 4 ILE A1000 VAL A1002 -1 O VAL A1002 N TYR A 985 LINK NE2 HIS A 756 ZN ZN A1106 1555 1555 2.16 LINK NE2 HIS A 760 ZN ZN A1106 1555 1555 2.16 LINK OE1 GLU A 771 ZN ZN A1106 1555 1555 2.03 LINK ZN ZN A1106 O HOH A1300 1555 1555 2.05 LINK ZN ZN A1106 O HOH A1312 1555 1555 2.04 SITE 1 AC1 5 GLY A 569 LYS A 570 SER A 932 LEU A 979 SITE 2 AC1 5 HOH A1319 SITE 1 AC2 6 PRO A 586 ASP A 588 VAL A 589 GLN A 666 SITE 2 AC2 6 HOH A1234 HOH A1245 SITE 1 AC3 5 ASP A 588 PRO A 647 LYS A 648 HOH A1510 SITE 2 AC3 5 HOH A1602 SITE 1 AC4 5 SER A 496 THR A 524 VAL A 611 ARG A 612 SITE 2 AC4 5 ILE A 613 SITE 1 AC5 5 TYR A 834 LEU A 835 ASN A 838 MET A 914 SITE 2 AC5 5 ASN A 915 SITE 1 AC6 5 HIS A 756 HIS A 760 GLU A 771 HOH A1300 SITE 2 AC6 5 HOH A1312 CRYST1 65.890 68.020 170.860 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.015177 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014702 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005853 0.00000