HEADER HYDROLASE/HYDROLASE INHIBITOR 06-AUG-15 5D2R TITLE INHIBITOR BOUND CELL SHAPE DETERMINANT PROTEIN CSD4 FROM HELICOBACTER TITLE 2 PYLORI COMPND MOL_ID: 1; COMPND 2 MOLECULE: CONSERVED HYPOTHETICAL SECRETED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_TAXID: 563041; SOURCE 4 STRAIN: G27; SOURCE 5 GENE: HPG27_353; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B(MOD) KEYWDS MIXED ALPHA BETA SANDWICH, CARBOXYPEPTIDASE, M14, HYDROLASE-HYDROLASE KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.C.CHAN,M.E.MURPHY REVDAT 3 27-SEP-23 5D2R 1 REMARK REVDAT 2 27-APR-16 5D2R 1 JRNL REVDAT 1 20-JAN-16 5D2R 0 JRNL AUTH Y.LIU,E.FRIRDICH,J.A.TAYLOR,A.C.CHAN,K.M.BLAIR,J.VERMEULEN, JRNL AUTH 2 R.HA,M.E.MURPHY,N.R.SALAMA,E.C.GAYNOR,M.E.TANNER JRNL TITL A BACTERIAL CELL SHAPE-DETERMINING INHIBITOR. JRNL REF ACS CHEM.BIOL. V. 11 981 2016 JRNL REFN ESSN 1554-8937 JRNL PMID 26735022 JRNL DOI 10.1021/ACSCHEMBIO.5B01039 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 41015 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2050 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 39.0358 - 4.6833 1.00 2795 147 0.1737 0.1878 REMARK 3 2 4.6833 - 3.7182 1.00 2657 139 0.1387 0.1725 REMARK 3 3 3.7182 - 3.2485 1.00 2641 139 0.1664 0.2141 REMARK 3 4 3.2485 - 2.9516 1.00 2603 137 0.1767 0.2475 REMARK 3 5 2.9516 - 2.7401 1.00 2599 137 0.1907 0.2374 REMARK 3 6 2.7401 - 2.5786 1.00 2579 136 0.1869 0.2407 REMARK 3 7 2.5786 - 2.4495 1.00 2592 136 0.1882 0.2067 REMARK 3 8 2.4495 - 2.3428 1.00 2604 137 0.1838 0.2396 REMARK 3 9 2.3428 - 2.2527 1.00 2562 135 0.1889 0.2488 REMARK 3 10 2.2527 - 2.1749 1.00 2561 135 0.2008 0.2215 REMARK 3 11 2.1749 - 2.1069 1.00 2546 134 0.2042 0.2781 REMARK 3 12 2.1069 - 2.0467 1.00 2564 135 0.2148 0.2314 REMARK 3 13 2.0467 - 1.9928 1.00 2574 136 0.2200 0.2183 REMARK 3 14 1.9928 - 1.9442 1.00 2547 134 0.2470 0.2650 REMARK 3 15 1.9442 - 1.9000 1.00 2541 133 0.2795 0.3513 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.790 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.89 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.79 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 : 0.009 3516 REMARK 3 ANGLE : 1.203 4754 REMARK 3 CHIRALITY : 0.051 514 REMARK 3 PLANARITY : 0.006 619 REMARK 3 DIHEDRAL : 14.250 1346 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 19 THROUGH 65 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.1345 40.6013 5.9651 REMARK 3 T TENSOR REMARK 3 T11: 0.1697 T22: 0.1007 REMARK 3 T33: 0.2557 T12: -0.0194 REMARK 3 T13: 0.0141 T23: -0.0278 REMARK 3 L TENSOR REMARK 3 L11: 0.4915 L22: 0.0190 REMARK 3 L33: 0.1548 L12: -0.0505 REMARK 3 L13: -0.1192 L23: -0.0557 REMARK 3 S TENSOR REMARK 3 S11: 0.1639 S12: -0.1283 S13: 0.2611 REMARK 3 S21: 0.0263 S22: -0.1463 S23: 0.0118 REMARK 3 S31: 0.0348 S32: -0.0987 S33: 0.0586 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 66 THROUGH 247 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.4924 31.7214 -5.9549 REMARK 3 T TENSOR REMARK 3 T11: 0.1242 T22: 0.1108 REMARK 3 T33: 0.1467 T12: 0.0034 REMARK 3 T13: 0.0077 T23: 0.0200 REMARK 3 L TENSOR REMARK 3 L11: 0.8642 L22: 0.5749 REMARK 3 L33: 1.1604 L12: 0.0467 REMARK 3 L13: 0.2837 L23: -0.2951 REMARK 3 S TENSOR REMARK 3 S11: 0.1387 S12: 0.1020 S13: 0.0928 REMARK 3 S21: -0.0757 S22: -0.0593 S23: -0.0073 REMARK 3 S31: 0.1337 S32: -0.1094 S33: 0.0766 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 248 THROUGH 339 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.3104 26.6536 20.1695 REMARK 3 T TENSOR REMARK 3 T11: 0.1537 T22: 0.2415 REMARK 3 T33: 0.1161 T12: -0.0766 REMARK 3 T13: -0.0103 T23: 0.0042 REMARK 3 L TENSOR REMARK 3 L11: 0.4396 L22: 0.2027 REMARK 3 L33: 1.0554 L12: 0.0688 REMARK 3 L13: 0.9043 L23: -0.0998 REMARK 3 S TENSOR REMARK 3 S11: 0.0273 S12: -0.2605 S13: 0.0542 REMARK 3 S21: 0.0031 S22: 0.0591 S23: -0.1176 REMARK 3 S31: 0.2202 S32: -0.4286 S33: 0.1115 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 340 THROUGH 438 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.5517 26.2164 42.6683 REMARK 3 T TENSOR REMARK 3 T11: 0.3045 T22: 0.4240 REMARK 3 T33: 0.1815 T12: 0.0002 REMARK 3 T13: -0.0325 T23: -0.0468 REMARK 3 L TENSOR REMARK 3 L11: 0.4270 L22: 0.3005 REMARK 3 L33: 1.1593 L12: 0.0515 REMARK 3 L13: 0.2967 L23: 0.2323 REMARK 3 S TENSOR REMARK 3 S11: 0.1820 S12: -0.0671 S13: 0.0783 REMARK 3 S21: 0.0648 S22: -0.0858 S23: -0.1654 REMARK 3 S31: 0.0673 S32: -0.4942 S33: 0.0045 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 5D2R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000212578. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-SEP-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 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) : 0.9796 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41021 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 39.030 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.2400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.83400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.580 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 4WCK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 13-18% PEG 3350, 0.015 MM TRIS PH 8 REMARK 280 AND 0.4 M NAI, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 26.42000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 72.24000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.30500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 72.24000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.42000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.30500 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 0 REMARK 465 GLY A 1 REMARK 465 SER A 2 REMARK 465 SER A 3 REMARK 465 HIS 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 SER A 10 REMARK 465 SER A 11 REMARK 465 GLY A 12 REMARK 465 LEU A 13 REMARK 465 VAL A 14 REMARK 465 PRO A 15 REMARK 465 ARG A 16 REMARK 465 GLY A 17 REMARK 465 SER A 18 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 HE2 HIS A 181 O HOH A 601 1.54 REMARK 500 O HOH A 779 O HOH A 820 2.17 REMARK 500 O HOH A 845 O HOH A 857 2.18 REMARK 500 O HOH A 693 O HOH A 721 2.19 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 ALA A 97 -121.74 -106.19 REMARK 500 ASN A 267 41.91 -94.13 REMARK 500 SER A 276 -135.25 48.56 REMARK 500 LYS A 319 -123.47 52.91 REMARK 500 ASN A 354 -8.40 80.14 REMARK 500 GLU A 369 -52.45 -133.58 REMARK 500 SER A 389 -141.81 -107.88 REMARK 500 ASN A 390 35.13 -145.28 REMARK 500 LYS A 425 70.73 -115.08 REMARK 500 ASN A 426 85.99 59.32 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 884 DISTANCE = 5.86 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 A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 46 OE1 REMARK 620 2 GLU A 49 OE1 95.6 REMARK 620 3 GLU A 49 OE2 85.6 55.2 REMARK 620 4 HIS A 128 ND1 94.8 106.1 161.2 REMARK 620 5 56W A 523 O2 88.5 138.3 84.0 114.8 REMARK 620 6 56W A 523 O6 154.4 105.4 94.3 93.3 66.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 62 ND1 REMARK 620 2 ASP A 254 OD1 97.8 REMARK 620 3 ASP A 254 OD2 148.5 56.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 157 OD1 REMARK 620 2 GLU A 158 OE1 90.4 REMARK 620 N 1 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 511 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 512 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 513 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 514 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 515 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 518 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 520 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 521 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 56W A 523 DBREF 5D2R A 23 438 UNP B5ZAD9 B5ZAD9_HELPG 23 438 SEQADV 5D2R MET A 0 UNP B5ZAD9 INITIATING METHIONINE SEQADV 5D2R GLY A 1 UNP B5ZAD9 EXPRESSION TAG SEQADV 5D2R SER A 2 UNP B5ZAD9 EXPRESSION TAG SEQADV 5D2R SER A 3 UNP B5ZAD9 EXPRESSION TAG SEQADV 5D2R HIS A 4 UNP B5ZAD9 EXPRESSION TAG SEQADV 5D2R HIS A 5 UNP B5ZAD9 EXPRESSION TAG SEQADV 5D2R HIS A 6 UNP B5ZAD9 EXPRESSION TAG SEQADV 5D2R HIS A 7 UNP B5ZAD9 EXPRESSION TAG SEQADV 5D2R HIS A 8 UNP B5ZAD9 EXPRESSION TAG SEQADV 5D2R HIS A 9 UNP B5ZAD9 EXPRESSION TAG SEQADV 5D2R SER A 10 UNP B5ZAD9 EXPRESSION TAG SEQADV 5D2R SER A 11 UNP B5ZAD9 EXPRESSION TAG SEQADV 5D2R GLY A 12 UNP B5ZAD9 EXPRESSION TAG SEQADV 5D2R LEU A 13 UNP B5ZAD9 EXPRESSION TAG SEQADV 5D2R VAL A 14 UNP B5ZAD9 EXPRESSION TAG SEQADV 5D2R PRO A 15 UNP B5ZAD9 EXPRESSION TAG SEQADV 5D2R ARG A 16 UNP B5ZAD9 EXPRESSION TAG SEQADV 5D2R GLY A 17 UNP B5ZAD9 EXPRESSION TAG SEQADV 5D2R SER A 18 UNP B5ZAD9 EXPRESSION TAG SEQADV 5D2R SER A 19 UNP B5ZAD9 EXPRESSION TAG SEQADV 5D2R MET A 20 UNP B5ZAD9 EXPRESSION TAG SEQADV 5D2R GLU A 21 UNP B5ZAD9 EXPRESSION TAG SEQADV 5D2R MET A 22 UNP B5ZAD9 EXPRESSION TAG SEQRES 1 A 439 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 439 LEU VAL PRO ARG GLY SER SER MET GLU MET ILE GLU LYS SEQRES 3 A 439 ALA PRO THR ASP LEU GLU ASP ARG ASP LYS ALA PRO HIS SEQRES 4 A 439 LEU LEU LEU LEU ALA GLY ILE GLN GLY ASP GLU PRO GLY SEQRES 5 A 439 GLY PHE ASN ALA THR ASN LEU PHE LEU MET HIS TYR SER SEQRES 6 A 439 VAL LEU LYS GLY LEU VAL GLU VAL VAL PRO VAL LEU ASN SEQRES 7 A 439 LYS PRO SER MET LEU ARG ASN HIS ARG GLY LEU TYR GLY SEQRES 8 A 439 ASP MET ASN ARG LYS PHE ALA ALA LEU ASP LYS LYS ASP SEQRES 9 A 439 PRO GLU TYR PRO THR ILE GLN GLU ILE LYS SER LEU ILE SEQRES 10 A 439 ALA LYS PRO ASN ILE ASP ALA VAL LEU HIS LEU HIS ASP SEQRES 11 A 439 GLY GLY GLY TYR TYR ARG PRO VAL TYR VAL ASP ALA MET SEQRES 12 A 439 LEU ASN PRO LYS ARG TRP GLY ASN CYS PHE ILE ILE ASP SEQRES 13 A 439 GLN ASP GLU VAL LYS GLY ALA LYS PHE PRO ASN LEU LEU SEQRES 14 A 439 ALA PHE ALA ASN ASN THR ILE GLU SER ILE ASN ALA HIS SEQRES 15 A 439 LEU LEU HIS PRO ILE GLU GLU TYR HIS LEU LYS ASN THR SEQRES 16 A 439 ARG THR ALA GLN GLY ASP THR GLU MET GLN LYS ALA LEU SEQRES 17 A 439 THR PHE TYR ALA ILE ASN GLN LYS LYS SER ALA PHE ALA SEQRES 18 A 439 ASN GLU ALA SER LYS GLU LEU PRO LEU ALA SER ARG VAL SEQRES 19 A 439 PHE TYR HIS LEU GLN ALA ILE GLU GLY LEU LEU ASN GLN SEQRES 20 A 439 LEU ASN ILE PRO PHE LYS ARG ASP PHE GLU LEU ASN PRO SEQRES 21 A 439 SER SER VAL HIS ALA LEU ILE ASN ASP LYS SER LEU TRP SEQRES 22 A 439 ALA LYS ILE SER SER LEU PRO LYS ILE PRO LEU PHE ASN SEQRES 23 A 439 LEU ARG PRO ARG LEU ASN HIS PHE PRO LEU PRO HIS ASN SEQRES 24 A 439 THR LYS ILE PRO GLN ILE PRO ILE GLU SER ASN ALA TYR SEQRES 25 A 439 ILE VAL GLY LEU VAL LYS ASN LYS GLN GLU VAL PHE LEU SEQRES 26 A 439 LYS TYR GLY ASN LYS LEU MET THR ARG LEU SER PRO PHE SEQRES 27 A 439 TYR ILE GLU PHE ASP PRO SER LEU GLU GLU VAL LYS MET SEQRES 28 A 439 GLN ILE ASP ASN LYS ASP GLN MET VAL LYS ILE GLY SER SEQRES 29 A 439 VAL VAL GLU VAL LYS GLU SER PHE TYR ILE HIS ALA MET SEQRES 30 A 439 ASP ASN ILE ARG ALA ASN VAL ILE GLY PHE SER VAL SER SEQRES 31 A 439 ASN GLU ASN LYS PRO ASN GLU ALA GLY TYR THR ILE ARG SEQRES 32 A 439 PHE LYS ASP PHE GLN LYS ARG PHE SER LEU ASP LYS GLN SEQRES 33 A 439 GLU ARG ILE TYR ARG ILE GLU PHE TYR LYS ASN ASN ALA SEQRES 34 A 439 PHE SER GLY MET ILE LEU VAL LYS PHE VAL HET ZN A 501 1 HET ZN A 502 1 HET ZN A 503 1 HET IOD A 504 1 HET IOD A 505 1 HET IOD A 506 1 HET IOD A 507 1 HET IOD A 508 1 HET IOD A 509 1 HET IOD A 510 1 HET IOD A 511 1 HET IOD A 512 1 HET IOD A 513 1 HET IOD A 514 1 HET IOD A 515 1 HET IOD A 516 1 HET IOD A 517 1 HET IOD A 518 1 HET IOD A 519 1 HET IOD A 520 1 HET IOD A 521 1 HET IOD A 522 1 HET 56W A 523 50 HETNAM ZN ZINC ION HETNAM IOD IODIDE ION HETNAM 56W (2R,6R)-2-{[(R)-[(3R)-3-(ACETYLAMINO)-3- HETNAM 2 56W CARBOXYPROPYL](HYDROXY)PHOSPHORYL]METHYL}-6- HETNAM 3 56W AMINOHEPTANEDIOIC ACID FORMUL 2 ZN 3(ZN 2+) FORMUL 5 IOD 19(I 1-) FORMUL 24 56W C14 H25 N2 O9 P FORMUL 25 HOH *284(H2 O) HELIX 1 AA1 ASP A 29 ALA A 36 5 8 HELIX 2 AA2 GLU A 49 HIS A 62 1 14 HELIX 3 AA3 ASN A 77 ARG A 83 1 7 HELIX 4 AA4 ASP A 91 LYS A 95 5 5 HELIX 5 AA5 GLU A 105 ALA A 117 1 13 HELIX 6 AA6 ASN A 166 ALA A 180 1 15 HELIX 7 AA7 HIS A 184 GLU A 188 5 5 HELIX 8 AA8 GLU A 202 LYS A 205 5 4 HELIX 9 AA9 ALA A 206 ASN A 213 1 8 HELIX 10 AB1 PRO A 228 ASN A 248 1 21 HELIX 11 AB2 ASN A 258 ASN A 267 1 10 HELIX 12 AB3 LYS A 300 ILE A 304 5 5 HELIX 13 AB4 LYS A 404 PHE A 406 5 3 HELIX 14 AB5 GLN A 407 SER A 411 5 5 SHEET 1 AA1 7 ILE A 23 LYS A 25 0 SHEET 2 AA1 7 LEU A 69 VAL A 73 -1 O VAL A 72 N ILE A 23 SHEET 3 AA1 7 HIS A 38 LEU A 42 1 N LEU A 41 O GLU A 71 SHEET 4 AA1 7 ALA A 123 GLY A 130 1 O LEU A 127 N LEU A 42 SHEET 5 AA1 7 SER A 217 SER A 224 1 O SER A 217 N VAL A 124 SHEET 6 AA1 7 CYS A 151 ILE A 154 -1 N ILE A 153 O ALA A 220 SHEET 7 AA1 7 HIS A 190 ASN A 193 1 O LYS A 192 N PHE A 152 SHEET 1 AA2 2 TYR A 63 VAL A 65 0 SHEET 2 AA2 2 PHE A 251 ARG A 253 -1 O LYS A 252 N SER A 64 SHEET 1 AA3 2 TYR A 133 TYR A 134 0 SHEET 2 AA3 2 LEU A 143 ASN A 144 1 O ASN A 144 N TYR A 133 SHEET 1 AA4 3 ILE A 281 PRO A 282 0 SHEET 2 AA4 3 TRP A 272 ILE A 275 -1 N ALA A 273 O ILE A 281 SHEET 3 AA4 3 ILE A 306 SER A 308 -1 O GLU A 307 N LYS A 274 SHEET 1 AA5 4 ARG A 289 PRO A 296 0 SHEET 2 AA5 4 LYS A 329 ILE A 339 1 O ARG A 333 N LEU A 290 SHEET 3 AA5 4 GLU A 321 TYR A 326 -1 N VAL A 322 O LEU A 334 SHEET 4 AA5 4 VAL A 313 ASN A 318 -1 N ASN A 318 O GLU A 321 SHEET 1 AA6 4 LYS A 355 LYS A 360 0 SHEET 2 AA6 4 GLU A 347 ILE A 352 -1 N VAL A 348 O VAL A 359 SHEET 3 AA6 4 SER A 370 ILE A 373 -1 O TYR A 372 N GLN A 351 SHEET 4 AA6 4 THR A 400 ARG A 402 -1 O ILE A 401 N PHE A 371 SHEET 1 AA7 4 VAL A 364 VAL A 367 0 SHEET 2 AA7 4 PHE A 429 PHE A 437 1 O LEU A 434 N VAL A 365 SHEET 3 AA7 4 ILE A 418 TYR A 424 -1 N PHE A 423 O GLY A 431 SHEET 4 AA7 4 ARG A 380 VAL A 383 -1 N ASN A 382 O GLU A 422 LINK OE1 GLN A 46 ZN ZN A 501 1555 1555 2.05 LINK OE1 GLU A 49 ZN ZN A 501 1555 1555 2.19 LINK OE2 GLU A 49 ZN ZN A 501 1555 1555 2.55 LINK ND1 HIS A 62 ZN ZN A 502 1555 1555 2.04 LINK ND1 HIS A 128 ZN ZN A 501 1555 1555 2.09 LINK OD1 ASP A 157 ZN ZN A 503 1555 1555 2.06 LINK OE1 GLU A 158 ZN ZN A 503 1555 1555 2.12 LINK OD1 ASP A 254 ZN ZN A 502 1555 1555 2.62 LINK OD2 ASP A 254 ZN ZN A 502 1555 1555 1.75 LINK ZN ZN A 501 O2 56W A 523 1555 1555 2.43 LINK ZN ZN A 501 O6 56W A 523 1555 1555 2.34 SITE 1 AC1 4 GLN A 46 GLU A 49 HIS A 128 56W A 523 SITE 1 AC2 2 HIS A 62 ASP A 254 SITE 1 AC3 2 ASP A 157 GLU A 158 SITE 1 AC4 2 ASN A 267 LYS A 329 SITE 1 AC5 1 GLN A 198 SITE 1 AC6 1 SER A 260 SITE 1 AC7 1 LYS A 325 SITE 1 AC8 1 SER A 64 SITE 1 AC9 1 LYS A 163 SITE 1 AD1 1 LYS A 319 SITE 1 AD2 1 LYS A 404 SITE 1 AD3 1 HOH A 868 SITE 1 AD4 25 GLN A 46 GLU A 49 ARG A 86 ASN A 93 SITE 2 AD4 25 ARG A 94 HIS A 126 HIS A 128 ASP A 129 SITE 3 AD4 25 GLY A 130 GLY A 131 TRP A 148 MET A 203 SITE 4 AD4 25 ALA A 206 LEU A 207 THR A 208 ALA A 220 SITE 5 AD4 25 GLU A 222 LYS A 225 ZN A 501 HOH A 610 SITE 6 AD4 25 HOH A 622 HOH A 671 HOH A 672 HOH A 697 SITE 7 AD4 25 HOH A 753 CRYST1 52.840 66.610 144.480 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 0.018925 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015013 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006921 0.00000