HEADER HYDROLASE 05-SEP-14 4WCN TITLE CRYSTAL STRUCTURE OF TRIPEPTIDE BOUND CELL SHAPE DETERMINANT CSD4 TITLE 2 PROTEIN FROM HELICOBACTER 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 EXPDTA X-RAY DIFFRACTION AUTHOR A.C.CHAN,M.E.MURPHY REVDAT 6 27-DEC-23 4WCN 1 REMARK REVDAT 5 22-NOV-17 4WCN 1 SOURCE KEYWDS JRNL REMARK REVDAT 4 25-FEB-15 4WCN 1 REMARK REVDAT 3 18-FEB-15 4WCN 1 JRNL REVDAT 2 31-DEC-14 4WCN 1 JRNL REVDAT 1 24-DEC-14 4WCN 0 JRNL AUTH A.C.CHAN,K.M.BLAIR,Y.LIU,E.FRIRDICH,E.C.GAYNOR,M.E.TANNER, JRNL AUTH 2 N.R.SALAMA,M.E.MURPHY JRNL TITL HELICAL SHAPE OF HELICOBACTER PYLORI REQUIRES AN ATYPICAL JRNL TITL 2 GLUTAMINE AS A ZINC LIGAND IN THE CARBOXYPEPTIDASE CSD4. JRNL REF J.BIOL.CHEM. V. 290 3622 2015 JRNL REFN ESSN 1083-351X JRNL PMID 25505267 JRNL DOI 10.1074/JBC.M114.624734 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.920 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 100395 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) : 0.177 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 5027 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 49.1655 - 5.4353 0.98 3122 172 0.2016 0.2436 REMARK 3 2 5.4353 - 4.3150 1.00 3183 173 0.1528 0.1904 REMARK 3 3 4.3150 - 3.7698 1.00 3177 168 0.1476 0.1906 REMARK 3 4 3.7698 - 3.4252 1.00 3190 162 0.1656 0.1955 REMARK 3 5 3.4252 - 3.1797 1.00 3193 167 0.1723 0.1964 REMARK 3 6 3.1797 - 2.9923 1.00 3184 169 0.1739 0.1567 REMARK 3 7 2.9923 - 2.8425 1.00 3209 167 0.1750 0.1863 REMARK 3 8 2.8425 - 2.7187 1.00 3205 169 0.1791 0.2256 REMARK 3 9 2.7187 - 2.6141 1.00 3183 166 0.1792 0.2372 REMARK 3 10 2.6141 - 2.5239 1.00 3165 165 0.1718 0.1740 REMARK 3 11 2.5239 - 2.4450 1.00 3232 168 0.1710 0.2214 REMARK 3 12 2.4450 - 2.3751 1.00 3144 163 0.1691 0.2119 REMARK 3 13 2.3751 - 2.3126 1.00 3181 172 0.1636 0.2145 REMARK 3 14 2.3126 - 2.2561 1.00 3255 170 0.1691 0.2016 REMARK 3 15 2.2561 - 2.2048 1.00 3164 168 0.1653 0.2053 REMARK 3 16 2.2048 - 2.1579 1.00 3192 170 0.1693 0.2046 REMARK 3 17 2.1579 - 2.1148 1.00 3183 172 0.1716 0.1857 REMARK 3 18 2.1148 - 2.0749 1.00 3210 167 0.1742 0.2098 REMARK 3 19 2.0749 - 2.0378 1.00 3175 169 0.1802 0.2007 REMARK 3 20 2.0378 - 2.0033 1.00 3230 168 0.1898 0.2411 REMARK 3 21 2.0033 - 1.9709 1.00 3141 163 0.1903 0.2415 REMARK 3 22 1.9709 - 1.9406 1.00 3216 169 0.1935 0.2005 REMARK 3 23 1.9406 - 1.9121 1.00 3195 170 0.2025 0.2372 REMARK 3 24 1.9121 - 1.8851 1.00 3213 172 0.2116 0.2171 REMARK 3 25 1.8851 - 1.8597 1.00 3144 164 0.2247 0.2264 REMARK 3 26 1.8597 - 1.8355 1.00 3216 167 0.2304 0.2841 REMARK 3 27 1.8355 - 1.8126 1.00 3180 171 0.2369 0.2805 REMARK 3 28 1.8126 - 1.7907 0.98 3125 161 0.2472 0.2755 REMARK 3 29 1.7907 - 1.7699 0.97 3104 163 0.2758 0.3007 REMARK 3 30 1.7699 - 1.7500 0.95 3057 162 0.2851 0.3012 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.260 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.12 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.38 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 : 0.011 3497 REMARK 3 ANGLE : 1.334 4729 REMARK 3 CHIRALITY : 0.059 511 REMARK 3 PLANARITY : 0.007 618 REMARK 3 DIHEDRAL : 13.414 1327 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND RESID 20:267 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.2413 33.5321 -2.9158 REMARK 3 T TENSOR REMARK 3 T11: 0.0938 T22: 0.0947 REMARK 3 T33: 0.1328 T12: 0.0007 REMARK 3 T13: 0.0079 T23: -0.0037 REMARK 3 L TENSOR REMARK 3 L11: 1.4086 L22: 1.2534 REMARK 3 L33: 2.1573 L12: -0.0555 REMARK 3 L13: -0.0609 L23: -0.3708 REMARK 3 S TENSOR REMARK 3 S11: 0.0766 S12: 0.0769 S13: 0.1063 REMARK 3 S21: -0.0681 S22: -0.0688 S23: -0.0000 REMARK 3 S31: 0.0392 S32: -0.1536 S33: 0.0115 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 268:438 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.5073 25.6578 34.4554 REMARK 3 T TENSOR REMARK 3 T11: 0.2109 T22: 0.2168 REMARK 3 T33: 0.1729 T12: -0.0508 REMARK 3 T13: -0.0129 T23: -0.0043 REMARK 3 L TENSOR REMARK 3 L11: 0.5019 L22: 0.8843 REMARK 3 L33: 3.8375 L12: -0.0459 REMARK 3 L13: 0.8969 L23: -0.1269 REMARK 3 S TENSOR REMARK 3 S11: 0.0028 S12: -0.1860 S13: 0.0188 REMARK 3 S21: 0.1637 S22: -0.0278 S23: 0.0339 REMARK 3 S31: 0.2183 S32: -0.4040 S33: 0.0245 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 4WCN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-SEP-14. REMARK 100 THE DEPOSITION ID IS D_1000203572. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-NOV-13 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 : 100396 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 49.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.3500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.51100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.850 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16-20% PEG 3350, 0-0.1 MM TRIS PH 8 REMARK 280 AND 0.3-0.4 M NAI, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 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 26.61500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 72.52500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.41500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 72.52500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.61500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.41500 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 465 SER A 389 REMARK 465 ASN A 390 REMARK 465 GLU A 391 REMARK 465 ASN A 392 REMARK 465 LYS A 393 REMARK 465 PRO A 394 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 748 O HOH A 926 2.01 REMARK 500 O HOH A 784 O HOH A 898 2.10 REMARK 500 O HOH A 798 O HOH A 843 2.14 REMARK 500 O HOH A 643 O HOH A 664 2.18 REMARK 500 OH TYR A 89 O HOH A 601 2.18 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 ASN A 77 69.54 -117.44 REMARK 500 ALA A 97 -119.07 -105.49 REMARK 500 VAL A 139 -65.42 -108.48 REMARK 500 GLN A 198 48.94 -89.73 REMARK 500 ASN A 267 36.89 -96.49 REMARK 500 SER A 276 -136.85 52.82 REMARK 500 LYS A 319 -123.50 52.26 REMARK 500 ASN A 354 -10.24 83.45 REMARK 500 GLU A 369 -60.42 -134.37 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 425 ASN A 426 -35.55 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 = 6.07 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 542 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 46 OE1 REMARK 620 2 GLU A 49 OE1 89.0 REMARK 620 3 GLU A 49 OE2 83.8 51.6 REMARK 620 4 HIS A 128 ND1 97.7 101.7 153.3 REMARK 620 N 1 2 3 REMARK 630 REMARK 630 MOLECULE TYPE: NULL REMARK 630 MOLECULE NAME: N-ACETYL-L-ALANYL-N-[(1S,5R)-5-AMINO-1,5- REMARK 630 DICARBOXYPENTYL]-D-GLUTAMINE REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 3KS A 545 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: ACT ALA FGA API REMARK 630 DETAILS: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 505 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 519 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 520 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 524 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 525 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 526 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 527 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 528 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 529 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 530 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 531 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 532 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 533 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 534 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 535 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 536 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 540 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 541 REMARK 800 REMARK 800 SITE_IDENTIFIER: AF1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 542 REMARK 800 REMARK 800 SITE_IDENTIFIER: AF2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 543 REMARK 800 REMARK 800 SITE_IDENTIFIER: AF3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 544 REMARK 800 REMARK 800 SITE_IDENTIFIER: AF4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 3KS A 545 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4WCK RELATED DB: PDB REMARK 900 RELATED ID: 4WCL RELATED DB: PDB REMARK 900 RELATED ID: 4WCM RELATED DB: PDB DBREF 4WCN A 23 438 UNP B5ZAD9 B5ZAD9_HELPG 23 438 SEQADV 4WCN MET A 0 UNP B5ZAD9 INITIATING METHIONINE SEQADV 4WCN GLY A 1 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCN SER A 2 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCN SER A 3 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCN HIS A 4 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCN HIS A 5 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCN HIS A 6 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCN HIS A 7 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCN HIS A 8 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCN HIS A 9 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCN SER A 10 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCN SER A 11 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCN GLY A 12 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCN LEU A 13 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCN VAL A 14 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCN PRO A 15 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCN ARG A 16 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCN GLY A 17 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCN SER A 18 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCN SER A 19 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCN MET A 20 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCN GLU A 21 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCN 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 IOD A 501 1 HET IOD A 502 1 HET IOD A 503 1 HET IOD A 504 2 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 2 HET IOD A 515 2 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 IOD A 523 1 HET IOD A 524 1 HET IOD A 525 1 HET IOD A 526 1 HET IOD A 527 1 HET IOD A 528 1 HET IOD A 529 1 HET IOD A 530 1 HET IOD A 531 1 HET IOD A 532 1 HET IOD A 533 1 HET IOD A 534 1 HET IOD A 535 1 HET IOD A 536 1 HET IOD A 537 1 HET IOD A 538 1 HET IOD A 539 1 HET IOD A 540 1 HET IOD A 541 1 HET ZN A 542 1 HET NA A 543 1 HET NA A 544 1 HET 3KS A 545 55 HETNAM IOD IODIDE ION HETNAM ZN ZINC ION HETNAM NA SODIUM ION HETNAM 3KS N-ACETYL-L-ALANYL-N-[(1S,5R)-5-AMINO-1,5- HETNAM 2 3KS DICARBOXYPENTYL]-D-GLUTAMINE FORMUL 2 IOD 41(I 1-) FORMUL 43 ZN ZN 2+ FORMUL 44 NA 2(NA 1+) FORMUL 46 3KS C17 H28 N4 O9 FORMUL 47 HOH *327(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 LYS A 118 1 14 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 ARG A 195 GLY A 199 5 5 HELIX 9 AA9 GLU A 202 LYS A 205 5 4 HELIX 10 AB1 ALA A 206 GLN A 214 1 9 HELIX 11 AB2 PRO A 228 ASN A 248 1 21 HELIX 12 AB3 ASN A 258 ASN A 267 1 10 HELIX 13 AB4 LYS A 300 ILE A 304 5 5 HELIX 14 AB5 LYS A 404 PHE A 406 5 3 HELIX 15 AB6 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 125 N LEU A 42 SHEET 5 AA1 7 SER A 217 SER A 224 1 O PHE A 219 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 SER A 335 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 GLY A 314 O LYS A 325 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 LYS A 436 N VAL A 367 SHEET 3 AA7 4 ILE A 418 TYR A 424 -1 N ILE A 421 O ILE A 433 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 542 1555 1555 2.01 LINK OE1 GLU A 49 ZN ZN A 542 1555 1555 2.40 LINK OE2 GLU A 49 ZN ZN A 542 1555 1555 2.61 LINK ND1 HIS A 128 ZN ZN A 542 1555 1555 2.48 LINK NA NA A 544 O HOH A 640 1555 4555 2.51 SITE 1 AC1 2 LYS A 319 NA A 544 SITE 1 AC2 1 ASN A 166 SITE 1 AC3 3 HIS A 263 ASN A 267 LYS A 329 SITE 1 AC4 1 LYS A 317 SITE 1 AC5 1 THR A 400 SITE 1 AC6 1 PHE A 341 SITE 1 AC7 1 GLN A 320 SITE 1 AC8 1 HIS A 292 SITE 1 AC9 2 ASN A 193 ARG A 195 SITE 1 AD1 2 SER A 64 HOH A 705 SITE 1 AD2 1 ARG A 409 SITE 1 AD3 2 TYR A 89 ARG A 147 SITE 1 AD4 1 IOD A 528 SITE 1 AD5 1 ARG A 253 SITE 1 AD6 3 ARG A 253 GLU A 256 LEU A 257 SITE 1 AD7 1 SER A 260 SITE 1 AD8 3 SER A 231 IOD A 524 HOH A 811 SITE 1 AD9 1 SER A 19 SITE 1 AE1 2 ARG A 147 3KS A 545 SITE 1 AE2 1 LYS A 269 SITE 1 AE3 2 SER A 344 LYS A 425 SITE 1 AE4 1 LYS A 300 SITE 1 AE5 2 GLN A 303 NA A 543 SITE 1 AE6 3 GLN A 351 ASN A 354 SER A 370 SITE 1 AE7 2 LYS A 404 HOH A 913 SITE 1 AE8 2 ALA A 26 VAL A 65 SITE 1 AE9 3 SER A 276 PRO A 296 PRO A 305 SITE 1 AF1 4 GLN A 46 GLU A 49 HIS A 128 HOH A 687 SITE 1 AF2 3 LYS A 300 PRO A 302 IOD A 534 SITE 1 AF3 3 ARG A 135 IOD A 502 HOH A 640 SITE 1 AF4 20 ARG A 86 ASN A 93 ARG A 94 HIS A 126 SITE 2 AF4 20 HIS A 128 GLY A 130 GLY A 131 TRP A 148 SITE 3 AF4 20 MET A 203 ALA A 206 LEU A 207 THR A 208 SITE 4 AF4 20 ALA A 220 GLU A 222 LYS A 225 IOD A 530 SITE 5 AF4 20 HOH A 678 HOH A 683 HOH A 792 HOH A 927 CRYST1 53.230 66.830 145.050 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 0.018786 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014963 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006894 0.00000