HEADER HYDROLASE 08-JUN-16 5KDS TITLE ZMPB METALLOPEPTIDASE IN COMPLEX WITH AN O-GLYCOPEPTIDE (A2,6- TITLE 2 SIALYLATED CORE-3 PENTAPEPTIDE). COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA2,6-SIALYLATED CORE-3 PENTAPEPTIDE; COMPND 3 CHAIN: G; COMPND 4 SYNONYM: BSM FRAGMENT; COMPND 5 OTHER_DETAILS: GLYCOPEPTIDE FRAGMENT DERIVED FROM BOVINE SUBMAXILLARY COMPND 6 MUCIN; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: F5/8 TYPE C DOMAIN PROTEIN; COMPND 9 CHAIN: A; COMPND 10 FRAGMENT: UNP RESIDUES 497-1003; COMPND 11 SYNONYM: METALLOPEPTIDASE; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: IN COMPLEX WITH A BSM FRAGMENT. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: CLOSTRIDIUM PERFRINGENS (STRAIN ATCC 13124 / SOURCE 7 DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / TYPE A); SOURCE 8 ORGANISM_TAXID: 195103; SOURCE 9 STRAIN: ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / SOURCE 10 TYPE A; SOURCE 11 GENE: CPF_1489; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS O-GLYCOPEPTIDASE, PF13402/M60-LIKE, BOVINE SUBMAXILLARY MUCIN, O- KEYWDS 2 GLYCAN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR I.NOACH,E.FICKO-BLEAN,C.STUART,A.B.BORASTON REVDAT 5 27-SEP-23 5KDS 1 HETSYN LINK REVDAT 4 29-JUL-20 5KDS 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 08-FEB-17 5KDS 1 JRNL REVDAT 2 01-FEB-17 5KDS 1 JRNL REVDAT 1 11-JAN-17 5KDS 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. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 94972 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) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4992 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5071 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 70.03 REMARK 3 BIN R VALUE (WORKING SET) : 0.2210 REMARK 3 BIN FREE R VALUE SET COUNT : 264 REMARK 3 BIN FREE R VALUE : 0.2380 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4121 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 94 REMARK 3 SOLVENT ATOMS : 794 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.51000 REMARK 3 B22 (A**2) : 1.91000 REMARK 3 B33 (A**2) : -1.40000 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): 0.068 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.071 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.044 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.259 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.958 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4342 ; 0.015 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5873 ; 1.657 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 528 ; 6.158 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 218 ;39.396 ;25.321 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 736 ;12.678 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;18.901 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 626 ; 0.118 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3325 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 2076 ; 1.602 ; 1.870 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2595 ; 2.437 ; 2.796 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2266 ; 2.740 ; 2.152 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 7769 ; 6.795 ;18.314 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 : 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 5KDS 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_1000222068. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUL-11 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 : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9790 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 99964 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 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 : 20.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.35400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.600 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 (%): 61.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 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 33.09000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 85.78500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.47500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 85.78500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.09000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.47500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: G, 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 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 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 1213 O HOH A 1793 2.07 REMARK 500 O7 SIA B 3 O HOH G 201 2.17 REMARK 500 O3 A2G B 1 O5 NAG B 2 2.18 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. = -3.7 DEGREES REMARK 500 ASP A 594 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG A 607 NE - CZ - NH2 ANGL. DEV. = -3.2 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 MET A 502 75.99 -119.92 REMARK 500 LYS A 626 -47.60 -130.60 REMARK 500 SER A 723 -163.59 -162.67 REMARK 500 VAL A 772 -68.21 -123.22 REMARK 500 ASN A 800 -50.45 -125.05 REMARK 500 ASN A 935 -120.32 40.01 REMARK 500 ASP A 980 40.31 -99.54 REMARK 500 VAL A1002 -78.38 -114.15 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 -146.92 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 A1986 DISTANCE = 5.87 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 A1101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 756 NE2 REMARK 620 2 HIS A 760 NE2 90.8 REMARK 620 3 GLU A 771 OE1 94.1 90.8 REMARK 620 4 TLA A1102 O11 92.5 173.0 82.8 REMARK 620 5 TLA A1102 O2 171.6 97.5 86.5 79.2 REMARK 620 6 HOH A1222 O 102.3 89.2 163.6 96.1 77.3 REMARK 620 N 1 2 3 4 5 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: 5KDN 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 DBREF 5KDS G 4 8 PDB 5KDS 5KDS 4 8 DBREF1 5KDS A 497 1003 UNP A0A0H2YN38_CLOP1 DBREF2 5KDS A A0A0H2YN38 497 1003 SEQADV 5KDS MET A 474 UNP A0A0H2YN3 INITIATING METHIONINE SEQADV 5KDS GLY A 475 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDS SER A 476 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDS SER A 477 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDS HIS A 478 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDS HIS A 479 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDS HIS A 480 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDS HIS A 481 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDS HIS A 482 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDS HIS A 483 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDS SER A 484 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDS SER A 485 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDS GLY A 486 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDS LEU A 487 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDS VAL A 488 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDS PRO A 489 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDS ARG A 490 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDS GLY A 491 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDS SER A 492 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDS HIS A 493 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDS MET A 494 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDS ALA A 495 UNP A0A0H2YN3 EXPRESSION TAG SEQADV 5KDS SER A 496 UNP A0A0H2YN3 EXPRESSION TAG SEQRES 1 G 5 THR ALA PRO GLY GLY 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 A2G B 1 14 HET NAG B 2 14 HET SIA B 3 20 HET ZN A1101 1 HET TLA A1102 10 HET EPE A1103 15 HET EDO A1104 4 HET EDO A1105 4 HET EDO A1106 4 HET EDO A1107 4 HET EDO A1108 4 HETNAM A2G 2-ACETAMIDO-2-DEOXY-ALPHA-D-GALACTOPYRANOSE HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM SIA N-ACETYL-ALPHA-NEURAMINIC ACID HETNAM ZN ZINC ION HETNAM TLA L(+)-TARTARIC ACID HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM EDO 1,2-ETHANEDIOL HETSYN A2G N-ACETYL-ALPHA-D-GALACTOSAMINE; 2-ACETAMIDO-2-DEOXY- HETSYN 2 A2G ALPHA-D-GALACTOSE; 2-ACETAMIDO-2-DEOXY-D-GALACTOSE; 2- HETSYN 3 A2G ACETAMIDO-2-DEOXY-GALACTOSE; N-ACETYL-2-DEOXY-2-AMINO- HETSYN 4 A2G GALACTOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN SIA N-ACETYLNEURAMINIC ACID; SIALIC ACID; ALPHA-SIALIC HETSYN 2 SIA ACID; O-SIALIC ACID HETSYN EPE HEPES HETSYN EDO ETHYLENE GLYCOL FORMUL 3 A2G C8 H15 N O6 FORMUL 3 NAG C8 H15 N O6 FORMUL 3 SIA C11 H19 N O9 FORMUL 4 ZN ZN 2+ FORMUL 5 TLA C4 H6 O6 FORMUL 6 EPE C8 H18 N2 O4 S FORMUL 7 EDO 5(C2 H6 O2) FORMUL 12 HOH *794(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 ASP A 539 O LYS A 610 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 GLU A1001 -1 O ILE A1000 N VAL A 987 LINK OG1 THR G 4 C1 A2G B 1 1555 1555 1.54 LINK O3 A2G B 1 C1 NAG B 2 1555 1555 1.43 LINK O6 A2G B 1 C2 SIA B 3 1555 1555 1.55 LINK NE2 HIS A 756 ZN ZN A1101 1555 1555 2.16 LINK NE2 HIS A 760 ZN ZN A1101 1555 1555 2.13 LINK OE1 GLU A 771 ZN ZN A1101 1555 1555 2.11 LINK ZN ZN A1101 O11 TLA A1102 1555 1555 1.99 LINK ZN ZN A1101 O2 TLA A1102 1555 1555 2.19 LINK ZN ZN A1101 O HOH A1222 1555 1555 2.23 CISPEP 1 GLY G 7 GLY G 8 0 3.45 CRYST1 66.180 68.950 171.570 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 0.015110 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014503 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005829 0.00000