HEADER OXIDOREDUCTASE 22-JUN-15 5C5T TITLE THE CRYSTAL STRUCTURE OF VIRAL COLLAGEN PROLYL HYDROXYLASE VCPH FROM TITLE 2 PARAMECIUM BURSARIA CHLORELLA VIRUS-1 - 2OG COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROLYL 4-HYDROXYLASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 36-242; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PARAMECIUM BURSARIA CHLORELLA VIRUS 1; SOURCE 3 ORGANISM_COMMON: PBCV-1; SOURCE 4 ORGANISM_TAXID: 10506; SOURCE 5 GENE: A085R; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-28A KEYWDS DIOXYGENASE, PROLYL HYDROXYLASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR C.W.LEVY REVDAT 4 20-NOV-24 5C5T 1 REMARK REVDAT 3 10-JAN-24 5C5T 1 LINK REVDAT 2 14-OCT-15 5C5T 1 JRNL REVDAT 1 30-SEP-15 5C5T 0 JRNL AUTH J.E.LONGBOTHAM,C.LEVY,L.O.JOHANNISSEN,H.TARHONSKAYA,S.JIANG, JRNL AUTH 2 C.LOENARZ,E.FLASHMAN,S.HAY,C.J.SCHOFIELD,N.S.SCRUTTON JRNL TITL STRUCTURE AND MECHANISM OF A VIRAL COLLAGEN PROLYL JRNL TITL 2 HYDROXYLASE. JRNL REF BIOCHEMISTRY V. 54 6093 2015 JRNL REFN ISSN 0006-2960 JRNL PMID 26368022 JRNL DOI 10.1021/ACS.BIOCHEM.5B00789 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_1977 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 55202 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.580 REMARK 3 FREE R VALUE TEST SET COUNT : 1978 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 28.4312 - 3.8491 0.97 3800 146 0.1733 0.1724 REMARK 3 2 3.8491 - 3.0563 0.97 3804 130 0.1702 0.2164 REMARK 3 3 3.0563 - 2.6703 0.98 3825 143 0.1795 0.2100 REMARK 3 4 2.6703 - 2.4263 0.97 3745 144 0.1727 0.2415 REMARK 3 5 2.4263 - 2.2525 0.97 3804 142 0.1705 0.1912 REMARK 3 6 2.2525 - 2.1197 0.99 3877 144 0.1642 0.2107 REMARK 3 7 2.1197 - 2.0136 0.99 3861 145 0.1650 0.2127 REMARK 3 8 2.0136 - 1.9260 0.99 3859 142 0.1730 0.1909 REMARK 3 9 1.9260 - 1.8518 0.99 3823 142 0.1852 0.2277 REMARK 3 10 1.8518 - 1.7879 0.99 3800 141 0.1852 0.2397 REMARK 3 11 1.7879 - 1.7320 0.96 3782 139 0.1972 0.2627 REMARK 3 12 1.7320 - 1.6825 0.98 3788 140 0.2085 0.2567 REMARK 3 13 1.6825 - 1.6382 0.99 3860 144 0.2224 0.2581 REMARK 3 14 1.6382 - 1.5983 0.93 3596 136 0.2411 0.2785 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.420 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.016 3008 REMARK 3 ANGLE : 1.483 4055 REMARK 3 CHIRALITY : 0.076 418 REMARK 3 PLANARITY : 0.008 516 REMARK 3 DIHEDRAL : 15.632 1156 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -2.4289 37.0732 -13.2288 REMARK 3 T TENSOR REMARK 3 T11: 0.0911 T22: 0.1160 REMARK 3 T33: 0.0944 T12: 0.0183 REMARK 3 T13: -0.0076 T23: 0.0047 REMARK 3 L TENSOR REMARK 3 L11: 0.4798 L22: 1.0257 REMARK 3 L33: 0.4862 L12: 0.4914 REMARK 3 L13: -0.2720 L23: -0.4654 REMARK 3 S TENSOR REMARK 3 S11: 0.0074 S12: 0.0153 S13: -0.0034 REMARK 3 S21: -0.0077 S22: -0.0006 S23: -0.0045 REMARK 3 S31: 0.0026 S32: 0.0112 S33: -0.0048 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5C5T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-JUN-15. REMARK 100 THE DEPOSITION ID IS D_1000211072. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55206 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.598 REMARK 200 RESOLUTION RANGE LOW (A) : 28.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.5500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 2JIG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M [IMIDAZOLE; MES MONOHYDRATE REMARK 280 (ACID)], 0.1 M AMINO ACIDS [0.2 M L-NA-GLUTAMATE; 0.2 M ALANINE REMARK 280 (RACEMIC); 0.2 M GLYCINE; 0.2M LYSINE HCL (RACEMIC); 0.2 M REMARK 280 SERINE (RACEMIC)], 30 % PEGMME 550 PEG 20K PH 6.5 [MORPHEUS HT96 REMARK 280 CONDITION H1, MOLECULAR DIMENSIONS] COMPLEX GENERATED BY SOAKING REMARK 280 CRYSTALS IN MOTHER LIQUOR SUPPLEMENTED WITH 250 MM ZNSO4 AND 100 REMARK 280 MM 2-OG FOR A PERIOD OF 16 HOURS., PH 7.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 277K 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 78.47500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 1 REMARK 465 GLY A 2 REMARK 465 SER A 3 REMARK 465 SER A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 HIS A 8 REMARK 465 HIS A 9 REMARK 465 HIS A 10 REMARK 465 SER A 11 REMARK 465 SER A 12 REMARK 465 GLY A 13 REMARK 465 LEU A 14 REMARK 465 VAL A 15 REMARK 465 PRO A 16 REMARK 465 ARG A 17 REMARK 465 GLY A 18 REMARK 465 SER A 19 REMARK 465 HIS A 20 REMARK 465 MET A 21 REMARK 465 GLU A 22 REMARK 465 GLY A 23 REMARK 465 PHE A 24 REMARK 465 GLU A 25 REMARK 465 THR A 26 REMARK 465 SER A 27 REMARK 465 ASP A 28 REMARK 465 ARG A 29 REMARK 465 PRO A 30 REMARK 465 LYS A 64 REMARK 465 SER A 65 REMARK 465 GLU A 66 REMARK 465 VAL A 67 REMARK 465 GLY A 68 REMARK 465 GLY A 69 REMARK 465 ALA A 70 REMARK 465 THR A 71 REMARK 465 GLU A 72 REMARK 465 ASN A 73 REMARK 465 ASP A 74 REMARK 465 PRO A 75 REMARK 465 ILE A 76 REMARK 465 LYS A 77 REMARK 465 LEU A 78 REMARK 465 ASP A 79 REMARK 465 LYS A 228 REMARK 465 MET B 1 REMARK 465 GLY B 2 REMARK 465 SER B 3 REMARK 465 SER B 4 REMARK 465 HIS B 5 REMARK 465 HIS B 6 REMARK 465 HIS B 7 REMARK 465 HIS B 8 REMARK 465 HIS B 9 REMARK 465 HIS B 10 REMARK 465 SER B 11 REMARK 465 SER B 12 REMARK 465 GLY B 13 REMARK 465 LEU B 14 REMARK 465 VAL B 15 REMARK 465 PRO B 16 REMARK 465 ARG B 17 REMARK 465 GLY B 18 REMARK 465 SER B 19 REMARK 465 HIS B 20 REMARK 465 MET B 21 REMARK 465 GLU B 22 REMARK 465 GLY B 23 REMARK 465 PHE B 24 REMARK 465 GLU B 25 REMARK 465 THR B 26 REMARK 465 SER B 27 REMARK 465 ASP B 28 REMARK 465 ARG B 29 REMARK 465 PRO B 30 REMARK 465 LYS B 64 REMARK 465 SER B 65 REMARK 465 GLU B 66 REMARK 465 VAL B 67 REMARK 465 GLY B 68 REMARK 465 GLY B 69 REMARK 465 ALA B 70 REMARK 465 THR B 71 REMARK 465 GLU B 72 REMARK 465 ASN B 73 REMARK 465 ASP B 74 REMARK 465 PRO B 75 REMARK 465 ILE B 76 REMARK 465 LYS B 77 REMARK 465 LEU B 78 REMARK 465 ASP B 79 REMARK 465 PRO B 80 REMARK 465 LYS B 81 REMARK 465 SER B 82 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 B 577 O HOH B 580 1.82 REMARK 500 O HOH B 518 O HOH B 536 1.84 REMARK 500 O HOH B 468 O HOH B 566 1.91 REMARK 500 O HOH B 401 O HOH B 454 1.92 REMARK 500 O HOH B 560 O HOH B 570 1.93 REMARK 500 OD2 ASP B 142 O HOH B 401 1.96 REMARK 500 O HOH B 420 O HOH B 477 1.97 REMARK 500 O HOH B 534 O HOH B 585 1.99 REMARK 500 O HOH B 530 O HOH B 539 2.01 REMARK 500 O HOH A 536 O HOH A 551 2.01 REMARK 500 NH1 ARG B 83 O HOH B 402 2.06 REMARK 500 O HOH B 457 O HOH B 575 2.07 REMARK 500 OE2 GLU B 165 O HOH B 403 2.07 REMARK 500 O HOH A 541 O HOH A 565 2.07 REMARK 500 O HOH B 416 O HOH B 549 2.07 REMARK 500 OD2 ASP A 117 O HOH A 401 2.07 REMARK 500 OD2 ASP B 34 O HOH B 404 2.12 REMARK 500 NE2 HIS B 114 O HOH B 404 2.14 REMARK 500 O HOH B 431 O HOH B 559 2.15 REMARK 500 O HOH A 420 O HOH A 500 2.17 REMARK 500 O HOH B 509 O HOH B 526 2.17 REMARK 500 OD2 ASP B 47 O HOH B 405 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 567 O HOH B 428 1455 2.02 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 LYS A 81 -106.90 -68.23 REMARK 500 SER A 82 -116.08 -65.37 REMARK 500 ASP A 117 -104.49 -97.95 REMARK 500 ASP A 145 -68.45 -131.27 REMARK 500 ARG A 199 17.00 58.94 REMARK 500 ASP B 34 14.79 59.77 REMARK 500 ASP B 117 -88.45 -106.56 REMARK 500 ASP B 145 -71.95 -128.12 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 LYS A 81 SER A 82 -149.50 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 A 592 DISTANCE = 6.47 ANGSTROMS REMARK 525 HOH A 593 DISTANCE = 6.98 ANGSTROMS REMARK 525 HOH A 594 DISTANCE = 8.07 ANGSTROMS REMARK 525 HOH B 600 DISTANCE = 6.53 ANGSTROMS REMARK 525 HOH B 601 DISTANCE = 7.44 ANGSTROMS REMARK 525 HOH B 602 DISTANCE = 7.77 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 MN A 303 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 34 OD1 REMARK 620 2 ASP A 34 OD2 54.1 REMARK 620 3 HIS A 114 NE2 89.5 120.4 REMARK 620 4 HOH A 446 O 135.8 83.9 102.8 REMARK 620 5 HOH A 548 O 145.6 136.1 101.5 73.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 138 NE2 REMARK 620 2 ASP A 140 OD1 97.7 REMARK 620 3 HIS A 207 NE2 99.4 93.0 REMARK 620 4 AKG A 301 O2 106.6 98.8 149.7 REMARK 620 5 AKG A 301 O5 94.6 167.7 85.7 76.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 138 NE2 REMARK 620 2 ASP B 140 OD1 96.8 REMARK 620 3 HIS B 207 NE2 97.4 96.7 REMARK 620 4 AKG B 301 O1 106.5 97.2 150.6 REMARK 620 5 AKG B 301 O5 96.2 167.0 81.4 79.3 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 AKG A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AKG B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 302 DBREF 5C5T A 22 228 UNP Q84406 Q84406_PBCV1 36 242 DBREF 5C5T B 22 228 UNP Q84406 Q84406_PBCV1 36 242 SEQADV 5C5T MET A 1 UNP Q84406 INITIATING METHIONINE SEQADV 5C5T GLY A 2 UNP Q84406 EXPRESSION TAG SEQADV 5C5T SER A 3 UNP Q84406 EXPRESSION TAG SEQADV 5C5T SER A 4 UNP Q84406 EXPRESSION TAG SEQADV 5C5T HIS A 5 UNP Q84406 EXPRESSION TAG SEQADV 5C5T HIS A 6 UNP Q84406 EXPRESSION TAG SEQADV 5C5T HIS A 7 UNP Q84406 EXPRESSION TAG SEQADV 5C5T HIS A 8 UNP Q84406 EXPRESSION TAG SEQADV 5C5T HIS A 9 UNP Q84406 EXPRESSION TAG SEQADV 5C5T HIS A 10 UNP Q84406 EXPRESSION TAG SEQADV 5C5T SER A 11 UNP Q84406 EXPRESSION TAG SEQADV 5C5T SER A 12 UNP Q84406 EXPRESSION TAG SEQADV 5C5T GLY A 13 UNP Q84406 EXPRESSION TAG SEQADV 5C5T LEU A 14 UNP Q84406 EXPRESSION TAG SEQADV 5C5T VAL A 15 UNP Q84406 EXPRESSION TAG SEQADV 5C5T PRO A 16 UNP Q84406 EXPRESSION TAG SEQADV 5C5T ARG A 17 UNP Q84406 EXPRESSION TAG SEQADV 5C5T GLY A 18 UNP Q84406 EXPRESSION TAG SEQADV 5C5T SER A 19 UNP Q84406 EXPRESSION TAG SEQADV 5C5T HIS A 20 UNP Q84406 EXPRESSION TAG SEQADV 5C5T MET A 21 UNP Q84406 EXPRESSION TAG SEQADV 5C5T MET B 1 UNP Q84406 INITIATING METHIONINE SEQADV 5C5T GLY B 2 UNP Q84406 EXPRESSION TAG SEQADV 5C5T SER B 3 UNP Q84406 EXPRESSION TAG SEQADV 5C5T SER B 4 UNP Q84406 EXPRESSION TAG SEQADV 5C5T HIS B 5 UNP Q84406 EXPRESSION TAG SEQADV 5C5T HIS B 6 UNP Q84406 EXPRESSION TAG SEQADV 5C5T HIS B 7 UNP Q84406 EXPRESSION TAG SEQADV 5C5T HIS B 8 UNP Q84406 EXPRESSION TAG SEQADV 5C5T HIS B 9 UNP Q84406 EXPRESSION TAG SEQADV 5C5T HIS B 10 UNP Q84406 EXPRESSION TAG SEQADV 5C5T SER B 11 UNP Q84406 EXPRESSION TAG SEQADV 5C5T SER B 12 UNP Q84406 EXPRESSION TAG SEQADV 5C5T GLY B 13 UNP Q84406 EXPRESSION TAG SEQADV 5C5T LEU B 14 UNP Q84406 EXPRESSION TAG SEQADV 5C5T VAL B 15 UNP Q84406 EXPRESSION TAG SEQADV 5C5T PRO B 16 UNP Q84406 EXPRESSION TAG SEQADV 5C5T ARG B 17 UNP Q84406 EXPRESSION TAG SEQADV 5C5T GLY B 18 UNP Q84406 EXPRESSION TAG SEQADV 5C5T SER B 19 UNP Q84406 EXPRESSION TAG SEQADV 5C5T HIS B 20 UNP Q84406 EXPRESSION TAG SEQADV 5C5T MET B 21 UNP Q84406 EXPRESSION TAG SEQRES 1 A 228 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 228 LEU VAL PRO ARG GLY SER HIS MET GLU GLY PHE GLU THR SEQRES 3 A 228 SER ASP ARG PRO GLY VAL CYS ASP GLY LYS TYR TYR GLU SEQRES 4 A 228 LYS ILE ASP GLY PHE LEU SER ASP ILE GLU CYS ASP VAL SEQRES 5 A 228 LEU ILE ASN ALA ALA ILE LYS LYS GLY LEU ILE LYS SER SEQRES 6 A 228 GLU VAL GLY GLY ALA THR GLU ASN ASP PRO ILE LYS LEU SEQRES 7 A 228 ASP PRO LYS SER ARG ASN SER GLU GLN THR TRP PHE MET SEQRES 8 A 228 PRO GLY GLU HIS GLU VAL ILE ASP LYS ILE GLN LYS LYS SEQRES 9 A 228 THR ARG GLU PHE LEU ASN SER LYS LYS HIS CYS ILE ASP SEQRES 10 A 228 LYS TYR ASN PHE GLU ASP VAL GLN VAL ALA ARG TYR LYS SEQRES 11 A 228 PRO GLY GLN TYR TYR TYR HIS HIS TYR ASP GLY ASP ASP SEQRES 12 A 228 CYS ASP ASP ALA CYS PRO LYS ASP GLN ARG LEU ALA THR SEQRES 13 A 228 LEU MET VAL TYR LEU LYS ALA PRO GLU GLU GLY GLY GLY SEQRES 14 A 228 GLY GLU THR ASP PHE PRO THR LEU LYS THR LYS ILE LYS SEQRES 15 A 228 PRO LYS LYS GLY THR SER ILE PHE PHE TRP VAL ALA ASP SEQRES 16 A 228 PRO VAL THR ARG LYS LEU TYR LYS GLU THR LEU HIS ALA SEQRES 17 A 228 GLY LEU PRO VAL LYS SER GLY GLU LYS ILE ILE ALA ASN SEQRES 18 A 228 GLN TRP ILE ARG ALA VAL LYS SEQRES 1 B 228 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 228 LEU VAL PRO ARG GLY SER HIS MET GLU GLY PHE GLU THR SEQRES 3 B 228 SER ASP ARG PRO GLY VAL CYS ASP GLY LYS TYR TYR GLU SEQRES 4 B 228 LYS ILE ASP GLY PHE LEU SER ASP ILE GLU CYS ASP VAL SEQRES 5 B 228 LEU ILE ASN ALA ALA ILE LYS LYS GLY LEU ILE LYS SER SEQRES 6 B 228 GLU VAL GLY GLY ALA THR GLU ASN ASP PRO ILE LYS LEU SEQRES 7 B 228 ASP PRO LYS SER ARG ASN SER GLU GLN THR TRP PHE MET SEQRES 8 B 228 PRO GLY GLU HIS GLU VAL ILE ASP LYS ILE GLN LYS LYS SEQRES 9 B 228 THR ARG GLU PHE LEU ASN SER LYS LYS HIS CYS ILE ASP SEQRES 10 B 228 LYS TYR ASN PHE GLU ASP VAL GLN VAL ALA ARG TYR LYS SEQRES 11 B 228 PRO GLY GLN TYR TYR TYR HIS HIS TYR ASP GLY ASP ASP SEQRES 12 B 228 CYS ASP ASP ALA CYS PRO LYS ASP GLN ARG LEU ALA THR SEQRES 13 B 228 LEU MET VAL TYR LEU LYS ALA PRO GLU GLU GLY GLY GLY SEQRES 14 B 228 GLY GLU THR ASP PHE PRO THR LEU LYS THR LYS ILE LYS SEQRES 15 B 228 PRO LYS LYS GLY THR SER ILE PHE PHE TRP VAL ALA ASP SEQRES 16 B 228 PRO VAL THR ARG LYS LEU TYR LYS GLU THR LEU HIS ALA SEQRES 17 B 228 GLY LEU PRO VAL LYS SER GLY GLU LYS ILE ILE ALA ASN SEQRES 18 B 228 GLN TRP ILE ARG ALA VAL LYS HET AKG A 301 10 HET ZN A 302 1 HET MN A 303 1 HET AKG B 301 10 HET ZN B 302 1 HETNAM AKG 2-OXOGLUTARIC ACID HETNAM ZN ZINC ION HETNAM MN MANGANESE (II) ION FORMUL 3 AKG 2(C5 H6 O5) FORMUL 4 ZN 2(ZN 2+) FORMUL 5 MN MN 2+ FORMUL 8 HOH *396(H2 O) HELIX 1 AA1 VAL A 32 LYS A 36 5 5 HELIX 2 AA2 SER A 46 LYS A 60 1 15 HELIX 3 AA3 HIS A 95 ASN A 110 1 16 HELIX 4 AA4 SER A 111 LYS A 113 5 3 HELIX 5 AA5 TYR A 202 LEU A 206 5 5 HELIX 6 AA6 VAL B 32 LYS B 36 5 5 HELIX 7 AA7 SER B 46 LYS B 60 1 15 HELIX 8 AA8 HIS B 95 ASN B 110 1 16 HELIX 9 AA9 SER B 111 LYS B 113 5 3 HELIX 10 AB1 TYR B 202 LEU B 206 5 5 SHEET 1 AA1 6 TYR A 38 ILE A 41 0 SHEET 2 AA1 6 SER A 188 TRP A 192 -1 O PHE A 190 N GLU A 39 SHEET 3 AA1 6 ARG A 153 LYS A 162 -1 N MET A 158 O ILE A 189 SHEET 4 AA1 6 LYS A 217 ARG A 225 -1 O ILE A 224 N LEU A 154 SHEET 5 AA1 6 GLN A 125 TYR A 129 -1 N GLN A 125 O ASN A 221 SHEET 6 AA1 6 GLU A 86 TRP A 89 -1 N THR A 88 O VAL A 126 SHEET 1 AA2 5 TYR A 38 ILE A 41 0 SHEET 2 AA2 5 SER A 188 TRP A 192 -1 O PHE A 190 N GLU A 39 SHEET 3 AA2 5 ARG A 153 LYS A 162 -1 N MET A 158 O ILE A 189 SHEET 4 AA2 5 LYS A 217 ARG A 225 -1 O ILE A 224 N LEU A 154 SHEET 5 AA2 5 ASN A 120 PHE A 121 -1 N ASN A 120 O ARG A 225 SHEET 1 AA3 5 ARG A 83 ASN A 84 0 SHEET 2 AA3 5 TYR A 134 HIS A 138 -1 O TYR A 134 N ASN A 84 SHEET 3 AA3 5 HIS A 207 GLY A 209 -1 O GLY A 209 N TYR A 135 SHEET 4 AA3 5 THR A 172 PHE A 174 -1 N ASP A 173 O ALA A 208 SHEET 5 AA3 5 THR A 179 ILE A 181 -1 O THR A 179 N PHE A 174 SHEET 1 AA4 6 TYR B 38 ILE B 41 0 SHEET 2 AA4 6 SER B 188 TRP B 192 -1 O PHE B 190 N GLU B 39 SHEET 3 AA4 6 ARG B 153 LYS B 162 -1 N MET B 158 O ILE B 189 SHEET 4 AA4 6 LYS B 217 ARG B 225 -1 O ILE B 224 N LEU B 154 SHEET 5 AA4 6 GLN B 125 TYR B 129 -1 N GLN B 125 O ASN B 221 SHEET 6 AA4 6 GLU B 86 TRP B 89 -1 N THR B 88 O VAL B 126 SHEET 1 AA5 5 TYR B 38 ILE B 41 0 SHEET 2 AA5 5 SER B 188 TRP B 192 -1 O PHE B 190 N GLU B 39 SHEET 3 AA5 5 ARG B 153 LYS B 162 -1 N MET B 158 O ILE B 189 SHEET 4 AA5 5 LYS B 217 ARG B 225 -1 O ILE B 224 N LEU B 154 SHEET 5 AA5 5 ASN B 120 PHE B 121 -1 N ASN B 120 O ARG B 225 SHEET 1 AA6 4 TYR B 135 HIS B 138 0 SHEET 2 AA6 4 HIS B 207 GLY B 209 -1 O GLY B 209 N TYR B 135 SHEET 3 AA6 4 THR B 172 PHE B 174 -1 N ASP B 173 O ALA B 208 SHEET 4 AA6 4 THR B 179 ILE B 181 -1 O ILE B 181 N THR B 172 SSBOND 1 CYS A 33 CYS A 115 1555 1555 2.06 SSBOND 2 CYS A 144 CYS A 148 1555 1555 2.05 SSBOND 3 CYS B 33 CYS B 115 1555 1555 2.04 SSBOND 4 CYS B 144 CYS B 148 1555 1555 2.03 LINK OD1 ASP A 34 MN MN A 303 1555 1555 2.60 LINK OD2 ASP A 34 MN MN A 303 1555 1555 2.20 LINK NE2 HIS A 114 MN MN A 303 1555 1555 2.01 LINK NE2 HIS A 138 ZN ZN A 302 1555 1555 2.10 LINK OD1 ASP A 140 ZN ZN A 302 1555 1555 2.02 LINK NE2 HIS A 207 ZN ZN A 302 1555 1555 2.10 LINK O2 AKG A 301 ZN ZN A 302 1555 1555 2.12 LINK O5 AKG A 301 ZN ZN A 302 1555 1555 2.25 LINK MN MN A 303 O HOH A 446 1555 1555 2.05 LINK MN MN A 303 O HOH A 548 1555 1555 2.33 LINK NE2 HIS B 138 ZN ZN B 302 1555 1555 2.09 LINK OD1 ASP B 140 ZN ZN B 302 1555 1555 2.01 LINK NE2 HIS B 207 ZN ZN B 302 1555 1555 2.05 LINK O1 AKG B 301 ZN ZN B 302 1555 1555 2.04 LINK O5 AKG B 301 ZN ZN B 302 1555 1555 2.31 SITE 1 AC1 15 TYR A 129 TYR A 135 HIS A 138 ASP A 140 SITE 2 AC1 15 THR A 172 HIS A 207 GLY A 209 LYS A 217 SITE 3 AC1 15 ILE A 219 ASN A 221 TRP A 223 ZN A 302 SITE 4 AC1 15 HOH A 430 HOH A 445 HOH A 519 SITE 1 AC2 4 HIS A 138 ASP A 140 HIS A 207 AKG A 301 SITE 1 AC3 4 ASP A 34 HIS A 114 HOH A 446 HOH A 548 SITE 1 AC4 15 TYR B 129 TYR B 135 HIS B 138 ASP B 140 SITE 2 AC4 15 THR B 172 HIS B 207 GLY B 209 LYS B 217 SITE 3 AC4 15 ILE B 219 ASN B 221 TRP B 223 ZN B 302 SITE 4 AC4 15 HOH B 441 HOH B 447 HOH B 488 SITE 1 AC5 4 HIS B 138 ASP B 140 HIS B 207 AKG B 301 CRYST1 33.790 156.950 41.240 90.00 90.02 90.00 P 1 21 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 0.029595 0.000000 0.000012 0.00000 SCALE2 0.000000 0.006371 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024248 0.00000