HEADER HYDROLASE 05-SEP-14 4WCL TITLE CRYSTAL STRUCTURE OF PRODUCT BOUND CELL SHAPE DETERMINANT PROTEIN CSD4 TITLE 2 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 15-NOV-23 4WCL 1 REMARK LINK ATOM REVDAT 5 22-NOV-17 4WCL 1 SOURCE KEYWDS JRNL REMARK REVDAT 4 25-FEB-15 4WCL 1 REMARK REVDAT 3 18-FEB-15 4WCL 1 JRNL REVDAT 2 31-DEC-14 4WCL 1 JRNL REVDAT 1 24-DEC-14 4WCL 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. 1.85 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.920 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 84283 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4210 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 42.7691 - 5.7440 0.97 2615 129 0.1981 0.2056 REMARK 3 2 5.7440 - 4.5609 0.99 2672 138 0.1601 0.1823 REMARK 3 3 4.5609 - 3.9848 1.00 2666 143 0.1287 0.1269 REMARK 3 4 3.9848 - 3.6207 1.00 2702 146 0.1456 0.1603 REMARK 3 5 3.6207 - 3.3613 1.00 2644 139 0.1559 0.1569 REMARK 3 6 3.3613 - 3.1632 1.00 2692 139 0.1545 0.2096 REMARK 3 7 3.1632 - 3.0048 1.00 2678 142 0.1695 0.2093 REMARK 3 8 3.0048 - 2.8741 1.00 2686 138 0.1642 0.1875 REMARK 3 9 2.8741 - 2.7634 1.00 2654 140 0.1636 0.2080 REMARK 3 10 2.7634 - 2.6681 1.00 2645 142 0.1608 0.1981 REMARK 3 11 2.6681 - 2.5847 1.00 2708 145 0.1623 0.2085 REMARK 3 12 2.5847 - 2.5108 1.00 2667 140 0.1601 0.2180 REMARK 3 13 2.5108 - 2.4447 1.00 2698 146 0.1617 0.1867 REMARK 3 14 2.4447 - 2.3851 1.00 2688 142 0.1596 0.2025 REMARK 3 15 2.3851 - 2.3309 1.00 2696 140 0.1635 0.1895 REMARK 3 16 2.3309 - 2.2813 1.00 2646 135 0.1640 0.2000 REMARK 3 17 2.2813 - 2.2356 1.00 2683 141 0.1694 0.2243 REMARK 3 18 2.2356 - 2.1934 1.00 2714 141 0.1676 0.2232 REMARK 3 19 2.1934 - 2.1543 1.00 2662 142 0.1711 0.1669 REMARK 3 20 2.1543 - 2.1177 1.00 2644 138 0.1707 0.2185 REMARK 3 21 2.1177 - 2.0836 0.99 2677 141 0.2007 0.2427 REMARK 3 22 2.0836 - 2.0515 0.95 2531 134 0.3009 0.3529 REMARK 3 23 2.0515 - 2.0214 1.00 2650 141 0.2044 0.2258 REMARK 3 24 2.0214 - 1.9929 1.00 2716 141 0.1999 0.2148 REMARK 3 25 1.9929 - 1.9660 1.00 2670 140 0.1903 0.2335 REMARK 3 26 1.9660 - 1.9404 1.00 2720 145 0.2042 0.2692 REMARK 3 27 1.9404 - 1.9162 1.00 2677 145 0.2080 0.2396 REMARK 3 28 1.9162 - 1.8931 1.00 2635 137 0.2145 0.2399 REMARK 3 29 1.8931 - 1.8711 1.00 2703 139 0.2243 0.2572 REMARK 3 30 1.8711 - 1.8500 0.98 2634 141 0.2312 0.2523 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.640 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.48 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.97 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 : 0.007 3477 REMARK 3 ANGLE : 1.089 4702 REMARK 3 CHIRALITY : 0.042 511 REMARK 3 PLANARITY : 0.005 612 REMARK 3 DIHEDRAL : 13.460 1321 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND RESID 20:50 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.6529 43.1946 4.8474 REMARK 3 T TENSOR REMARK 3 T11: 0.1474 T22: 0.1275 REMARK 3 T33: 0.2331 T12: 0.0020 REMARK 3 T13: 0.0348 T23: -0.0226 REMARK 3 L TENSOR REMARK 3 L11: 1.4156 L22: 2.7175 REMARK 3 L33: 1.4514 L12: 0.3937 REMARK 3 L13: 0.2745 L23: 0.1173 REMARK 3 S TENSOR REMARK 3 S11: 0.1293 S12: -0.1952 S13: 0.3588 REMARK 3 S21: 0.2878 S22: -0.1223 S23: 0.1059 REMARK 3 S31: -0.1783 S32: -0.1874 S33: 0.0004 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 51:277 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.3165 32.2919 -2.8193 REMARK 3 T TENSOR REMARK 3 T11: 0.1094 T22: 0.0893 REMARK 3 T33: 0.1473 T12: -0.0104 REMARK 3 T13: -0.0031 T23: -0.0094 REMARK 3 L TENSOR REMARK 3 L11: 1.0614 L22: 1.1886 REMARK 3 L33: 2.2852 L12: -0.1630 REMARK 3 L13: 0.2248 L23: -0.4593 REMARK 3 S TENSOR REMARK 3 S11: 0.0929 S12: 0.1132 S13: 0.0093 REMARK 3 S21: -0.1264 S22: -0.0371 S23: 0.0533 REMARK 3 S31: 0.2028 S32: -0.1225 S33: -0.0304 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 278:438 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.0643 25.4460 35.0836 REMARK 3 T TENSOR REMARK 3 T11: 0.1806 T22: 0.2399 REMARK 3 T33: 0.1423 T12: -0.0353 REMARK 3 T13: -0.0112 T23: -0.0069 REMARK 3 L TENSOR REMARK 3 L11: 0.3240 L22: 0.9957 REMARK 3 L33: 5.1216 L12: 0.0771 REMARK 3 L13: 0.7206 L23: 0.1806 REMARK 3 S TENSOR REMARK 3 S11: 0.0181 S12: -0.2186 S13: 0.0255 REMARK 3 S21: 0.1702 S22: -0.0128 S23: 0.0334 REMARK 3 S31: 0.3007 S32: -0.5188 S33: -0.0129 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 4WCL 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_1000203570. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUN-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) : 0.9795 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 : 84317 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 42.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.5300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.38800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.130 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT 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 (%): 53.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16-20% PEG 3350, 0-0.1 MM TRIS AND 0.3 REMARK 280 -0.4 M NAI, PH 8, 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 26.51500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 72.28500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.38500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 72.28500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.51500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.38500 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 393 CG CD CE NZ 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 HE21 GLN A 351 O HOH A 605 1.59 REMARK 500 OE1 GLU A 24 HH22 ARG A 33 1.60 REMARK 500 O HOH A 728 O HOH A 933 2.09 REMARK 500 O HOH A 777 O HOH A 882 2.12 REMARK 500 O HOH A 918 O HOH A 920 2.13 REMARK 500 O HOH A 724 O HOH A 747 2.14 REMARK 500 O HOH A 876 O HOH A 960 2.14 REMARK 500 O HOH A 625 O HOH A 649 2.16 REMARK 500 O HOH A 843 O HOH A 877 2.18 REMARK 500 O HOH A 744 O HOH A 849 2.18 REMARK 500 O HOH A 648 O HOH A 658 2.19 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 660 O HOH A 663 2564 2.11 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 -118.22 -107.26 REMARK 500 ASN A 267 45.70 -96.68 REMARK 500 SER A 276 -133.97 53.75 REMARK 500 LYS A 319 -116.09 52.57 REMARK 500 ASN A 354 -13.66 89.75 REMARK 500 GLU A 369 -57.66 -132.23 REMARK 500 REMARK 500 REMARK: NULL 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 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 46 OE1 REMARK 620 2 GLU A 49 OE1 97.2 REMARK 620 3 GLU A 49 OE2 91.3 57.3 REMARK 620 4 HIS A 128 ND1 92.4 95.2 152.5 REMARK 620 5 HOH A 702 O 161.6 94.2 82.6 101.0 REMARK 620 6 HOH A 746 O 83.8 155.8 98.5 109.0 79.9 REMARK 620 N 1 2 3 4 5 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 HIS A 62 ND1 REMARK 620 2 ASP A 254 OD1 90.9 REMARK 620 3 ASP A 254 OD2 133.0 55.3 REMARK 620 4 HOH A 778 O 97.6 74.4 102.1 REMARK 620 5 HOH A 962 O 109.4 159.3 105.5 105.8 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 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 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 511 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 513 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 514 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 515 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 516 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 517 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 518 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 521 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 522 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 526 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 527 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 529 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 530 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 534 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue API A 535 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 536 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4WCK RELATED DB: PDB REMARK 900 RELATED ID: 4WCM RELATED DB: PDB REMARK 900 RELATED ID: 4WCN RELATED DB: PDB DBREF 4WCL A 23 438 UNP B5ZAD9 B5ZAD9_HELPG 23 438 SEQADV 4WCL MET A 0 UNP B5ZAD9 INITIATING METHIONINE SEQADV 4WCL GLY A 1 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCL SER A 2 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCL SER A 3 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCL HIS A 4 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCL HIS A 5 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCL HIS A 6 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCL HIS A 7 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCL HIS A 8 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCL HIS A 9 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCL SER A 10 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCL SER A 11 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCL GLY A 12 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCL LEU A 13 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCL VAL A 14 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCL PRO A 15 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCL ARG A 16 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCL GLY A 17 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCL SER A 18 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCL SER A 19 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCL MET A 20 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCL GLU A 21 UNP B5ZAD9 EXPRESSION TAG SEQADV 4WCL 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 2 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 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 2 HET IOD A 533 1 HET IOD A 534 1 HET API A 535 25 HET NA A 536 1 HETNAM ZN ZINC ION HETNAM IOD IODIDE ION HETNAM API 2,6-DIAMINOPIMELIC ACID HETNAM NA SODIUM ION FORMUL 2 ZN 3(ZN 2+) FORMUL 5 IOD 31(I 1-) FORMUL 36 API C7 H14 N2 O4 FORMUL 37 NA NA 1+ FORMUL 38 HOH *401(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 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 ASN A 213 1 8 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 127 N LEU A 42 SHEET 5 AA1 7 SER A 217 SER A 224 1 O ASN A 221 N HIS A 128 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 PHE A 337 N PHE A 293 SHEET 3 AA5 4 GLU A 321 TYR A 326 -1 N LEU A 324 O MET A 331 SHEET 4 AA5 4 VAL A 313 ASN A 318 -1 N VAL A 316 O PHE A 323 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 ALA A 428 PHE A 437 1 O LEU A 434 N VAL A 365 SHEET 3 AA7 4 ILE A 418 LYS A 425 -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 502 1555 1555 2.22 LINK OE1 GLU A 49 ZN ZN A 502 1555 1555 2.30 LINK OE2 GLU A 49 ZN ZN A 502 1555 1555 2.30 LINK ND1 HIS A 62 ZN ZN A 501 1555 1555 1.95 LINK ND1 HIS A 128 ZN ZN A 502 1555 1555 2.02 LINK OD1 ASP A 254 ZN ZN A 501 1555 1555 2.64 LINK OD2 ASP A 254 ZN ZN A 501 1555 1555 1.76 LINK SD MET A 358 ZN ZN A 503 1555 1555 2.53 LINK ZN ZN A 501 O HOH A 778 1555 1555 2.49 LINK ZN ZN A 501 O HOH A 962 1555 1555 2.19 LINK ZN ZN A 502 O HOH A 702 1555 1555 2.31 LINK ZN ZN A 502 O HOH A 746 1555 1555 2.17 CISPEP 1 ASN A 426 ASN A 427 0 8.00 SITE 1 AC1 4 HIS A 62 ASP A 254 HOH A 778 HOH A 962 SITE 1 AC2 5 GLN A 46 GLU A 49 HIS A 128 HOH A 702 SITE 2 AC2 5 HOH A 746 SITE 1 AC3 4 MET A 358 IOD A 526 IOD A 527 IOD A 532 SITE 1 AC4 1 GLN A 303 SITE 1 AC5 1 ARG A 83 SITE 1 AC6 3 HIS A 263 ASN A 267 LYS A 329 SITE 1 AC7 1 LYS A 317 SITE 1 AC8 1 LYS A 319 SITE 1 AC9 1 PHE A 341 SITE 1 AD1 1 GLN A 198 SITE 1 AD2 1 ARG A 147 SITE 1 AD3 2 SER A 64 HOH A 889 SITE 1 AD4 1 PRO A 119 SITE 1 AD5 1 GLU A 187 SITE 1 AD6 1 LYS A 325 SITE 1 AD7 1 NA A 536 SITE 1 AD8 1 ZN A 503 SITE 1 AD9 2 LYS A 349 ZN A 503 SITE 1 AE1 1 SER A 19 SITE 1 AE2 1 SER A 260 SITE 1 AE3 2 LYS A 349 ZN A 503 SITE 1 AE4 2 THR A 400 HOH A 641 SITE 1 AE5 15 ASN A 93 ARG A 94 HIS A 126 HIS A 128 SITE 2 AE5 15 TRP A 148 MET A 203 ALA A 206 LEU A 207 SITE 3 AE5 15 THR A 208 ALA A 220 GLU A 222 HOH A 706 SITE 4 AE5 15 HOH A 726 HOH A 754 HOH A 764 SITE 1 AE6 2 HIS A 38 IOD A 522 CRYST1 53.030 66.770 144.570 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 0.018857 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014977 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006917 0.00000