HEADER HYDROLASE 16-DEC-13 4O23 TITLE CRYSTAL STRUCTURE OF MONO-ZINC FORM OF SUCCINYL DIAMINOPIMELATE TITLE 2 DESUCCINYLASE FROM NEISSERIA MENINGITIDIS MC58 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUCCINYL-DIAMINOPIMELATE DESUCCINYLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: SDAP DESUCCINYLASE, N-SUCCINYL-LL-2,6-DIAMINOHEPTANEDIOATE COMPND 5 AMIDOHYDROLASE; COMPND 6 EC: 3.5.1.18; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEISSERIA MENINGITIDIS; SOURCE 3 ORGANISM_TAXID: 122586; SOURCE 4 STRAIN: MC58; SOURCE 5 GENE: DAPE, NMB1530; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS DAPE, STRUCTURAL GENOMICS, CENTER FOR STRUCTURAL GENOMICS OF KEYWDS 2 INFECTIOUS DISEASES, CSGID, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR B.NOCEK,R.HOLZ,W.F.ANDERSON,A.JOACHIMIAK,CENTER FOR STRUCTURAL AUTHOR 2 GENOMICS OF INFECTIOUS DISEASES (CSGID) REVDAT 3 20-SEP-23 4O23 1 REMARK SEQADV LINK REVDAT 2 27-JAN-16 4O23 1 JRNL REVDAT 1 15-JAN-14 4O23 0 JRNL AUTH A.STARUS,B.NOCEK,B.BENNETT,J.A.LARRABEE,D.L.SHAW,W.SAE-LEE, JRNL AUTH 2 M.T.RUSSO,D.M.GILLNER,M.MAKOWSKA-GRZYSKA,A.JOACHIMIAK, JRNL AUTH 3 R.C.HOLZ JRNL TITL INHIBITION OF THE DAPE-ENCODED N-SUCCINYL-L,L-DIAMINOPIMELIC JRNL TITL 2 ACID DESUCCINYLASE FROM NEISSERIA MENINGITIDIS BY JRNL TITL 3 L-CAPTOPRIL. JRNL REF BIOCHEMISTRY V. 54 4834 2015 JRNL REFN ISSN 0006-2960 JRNL PMID 26186504 JRNL DOI 10.1021/ACS.BIOCHEM.5B00475 REMARK 2 REMARK 2 RESOLUTION. 2.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) 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) : 2.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.25 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.0 REMARK 3 NUMBER OF REFLECTIONS : 44283 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 2219 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 39.2572 - 5.2630 0.62 3473 171 0.1998 0.2116 REMARK 3 2 5.2630 - 4.1789 0.54 3010 167 0.1579 0.2053 REMARK 3 3 4.1789 - 3.6511 0.53 2955 149 0.1791 0.2056 REMARK 3 4 3.6511 - 3.3175 0.53 2966 146 0.1963 0.2389 REMARK 3 5 3.3175 - 3.0798 0.52 2876 170 0.2180 0.2159 REMARK 3 6 3.0798 - 2.8983 0.52 2934 149 0.2281 0.2736 REMARK 3 7 2.8983 - 2.7532 0.52 2884 153 0.2325 0.2375 REMARK 3 8 2.7532 - 2.6333 0.52 2887 136 0.2337 0.2470 REMARK 3 9 2.6333 - 2.5320 0.52 2878 170 0.2520 0.2969 REMARK 3 10 2.5320 - 2.4446 0.51 2849 154 0.2552 0.2928 REMARK 3 11 2.4446 - 2.3682 0.49 2697 156 0.2524 0.3119 REMARK 3 12 2.3682 - 2.3005 0.43 2360 117 0.2492 0.2664 REMARK 3 13 2.3005 - 2.2400 0.38 2161 105 0.2558 0.2944 REMARK 3 14 2.2400 - 2.1853 0.34 1886 123 0.2666 0.3000 REMARK 3 15 2.1853 - 2.1356 0.31 1766 71 0.2591 0.2960 REMARK 3 16 2.1356 - 2.0900 0.27 1482 82 0.2690 0.3025 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) : 25.740 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 : 0.003 5791 REMARK 3 ANGLE : 0.714 7877 REMARK 3 CHIRALITY : 0.027 901 REMARK 3 PLANARITY : 0.002 1039 REMARK 3 DIHEDRAL : 11.957 2093 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND (RESID 2:132) REMARK 3 ORIGIN FOR THE GROUP (A): -19.1341 -11.7185 -2.0003 REMARK 3 T TENSOR REMARK 3 T11: 0.2052 T22: 0.2528 REMARK 3 T33: 0.1192 T12: -0.0135 REMARK 3 T13: 0.0110 T23: 0.0258 REMARK 3 L TENSOR REMARK 3 L11: 1.8451 L22: 3.1611 REMARK 3 L33: 1.4736 L12: -0.1520 REMARK 3 L13: 0.3882 L23: 0.4378 REMARK 3 S TENSOR REMARK 3 S11: -0.0034 S12: -0.3398 S13: 0.0824 REMARK 3 S21: 0.2734 S22: -0.0529 S23: -0.0585 REMARK 3 S31: -0.0160 S32: -0.1775 S33: 0.0453 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND (RESID 133:173) REMARK 3 ORIGIN FOR THE GROUP (A): -8.5522 -15.0714 -9.7721 REMARK 3 T TENSOR REMARK 3 T11: 0.2331 T22: 0.2112 REMARK 3 T33: 0.2322 T12: -0.0415 REMARK 3 T13: 0.0072 T23: 0.0629 REMARK 3 L TENSOR REMARK 3 L11: 3.4468 L22: 2.2901 REMARK 3 L33: 3.2150 L12: -1.1159 REMARK 3 L13: 1.5831 L23: -0.8610 REMARK 3 S TENSOR REMARK 3 S11: 0.0336 S12: -0.0330 S13: 0.4031 REMARK 3 S21: 0.1150 S22: -0.2200 S23: -0.4029 REMARK 3 S31: -0.1457 S32: 0.2885 S33: 0.2127 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND (RESID 174:300) REMARK 3 ORIGIN FOR THE GROUP (A): 11.3541 3.3481 -23.0472 REMARK 3 T TENSOR REMARK 3 T11: 0.3302 T22: 0.2399 REMARK 3 T33: 0.4937 T12: -0.0689 REMARK 3 T13: -0.2014 T23: 0.1371 REMARK 3 L TENSOR REMARK 3 L11: 2.0098 L22: 1.7244 REMARK 3 L33: 0.3885 L12: 1.7891 REMARK 3 L13: -0.2744 L23: -0.1951 REMARK 3 S TENSOR REMARK 3 S11: 0.2526 S12: -0.2633 S13: -0.8581 REMARK 3 S21: 0.6157 S22: -0.2919 S23: -1.0454 REMARK 3 S31: -0.0984 S32: 0.1536 S33: 0.0359 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND (RESID 301:377) REMARK 3 ORIGIN FOR THE GROUP (A): -18.5781 -10.6328 -16.5508 REMARK 3 T TENSOR REMARK 3 T11: 0.1960 T22: 0.1509 REMARK 3 T33: 0.1604 T12: 0.0163 REMARK 3 T13: -0.0222 T23: 0.0520 REMARK 3 L TENSOR REMARK 3 L11: 1.0067 L22: 1.0095 REMARK 3 L33: 1.6833 L12: 0.0235 REMARK 3 L13: -0.2256 L23: 0.7360 REMARK 3 S TENSOR REMARK 3 S11: 0.0572 S12: -0.0159 S13: 0.0716 REMARK 3 S21: -0.1038 S22: -0.1452 S23: -0.0395 REMARK 3 S31: -0.1684 S32: -0.1822 S33: 0.0855 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN B AND (RESID 5:102) REMARK 3 ORIGIN FOR THE GROUP (A): 37.2926 43.8078 -3.7075 REMARK 3 T TENSOR REMARK 3 T11: 0.4508 T22: 1.0270 REMARK 3 T33: 0.5243 T12: -0.0901 REMARK 3 T13: 0.0265 T23: -0.2504 REMARK 3 L TENSOR REMARK 3 L11: 3.0571 L22: 1.7691 REMARK 3 L33: 2.1272 L12: 0.1601 REMARK 3 L13: -0.3031 L23: 0.8141 REMARK 3 S TENSOR REMARK 3 S11: 0.1603 S12: -0.9920 S13: 0.0044 REMARK 3 S21: 0.3195 S22: 0.4295 S23: -0.3211 REMARK 3 S31: -0.3011 S32: 1.0887 S33: -0.3009 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN B AND (RESID 103:173) REMARK 3 ORIGIN FOR THE GROUP (A): 37.8326 49.0850 -14.1895 REMARK 3 T TENSOR REMARK 3 T11: 0.4764 T22: 1.0086 REMARK 3 T33: 0.5901 T12: -0.3404 REMARK 3 T13: 0.2175 T23: -0.2978 REMARK 3 L TENSOR REMARK 3 L11: 2.5442 L22: 1.5844 REMARK 3 L33: 0.9797 L12: -0.2617 REMARK 3 L13: 0.4336 L23: -0.7254 REMARK 3 S TENSOR REMARK 3 S11: -0.0843 S12: -0.1922 S13: 0.2125 REMARK 3 S21: -0.3830 S22: 0.4686 S23: -0.1653 REMARK 3 S31: -0.8560 S32: 0.8885 S33: -0.3355 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN B AND (RESID 174:300) REMARK 3 ORIGIN FOR THE GROUP (A): 14.9692 25.7514 -26.7234 REMARK 3 T TENSOR REMARK 3 T11: 0.2659 T22: 0.1735 REMARK 3 T33: 0.1409 T12: -0.0634 REMARK 3 T13: -0.0280 T23: 0.0143 REMARK 3 L TENSOR REMARK 3 L11: 1.8539 L22: 2.6761 REMARK 3 L33: 1.2210 L12: 1.0303 REMARK 3 L13: -0.1002 L23: 0.3336 REMARK 3 S TENSOR REMARK 3 S11: 0.3208 S12: -0.1737 S13: 0.0521 REMARK 3 S21: 0.4545 S22: -0.2036 S23: -0.0682 REMARK 3 S31: -0.2558 S32: 0.2052 S33: -0.0711 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN B AND (RESID 301:376) REMARK 3 ORIGIN FOR THE GROUP (A): 43.2877 40.7429 -18.9246 REMARK 3 T TENSOR REMARK 3 T11: 0.4081 T22: 1.1565 REMARK 3 T33: 0.7001 T12: -0.4251 REMARK 3 T13: 0.1539 T23: -0.2890 REMARK 3 L TENSOR REMARK 3 L11: 1.7047 L22: 1.6650 REMARK 3 L33: 0.8840 L12: 1.4229 REMARK 3 L13: -0.4697 L23: 0.2015 REMARK 3 S TENSOR REMARK 3 S11: -0.0141 S12: -0.4413 S13: 0.0070 REMARK 3 S21: -0.3775 S22: 0.6839 S23: -0.6188 REMARK 3 S31: -0.2404 S32: 1.2000 S33: 0.0617 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 4O23 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-DEC-13. REMARK 100 THE DEPOSITION ID IS D_1000083944. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-NOV-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48738 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.090 REMARK 200 RESOLUTION RANGE LOW (A) : 39.250 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.09 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.7 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 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: MOLREP CCP4 REMARK 200 STARTING MODEL: PDB ENTRY 1VGY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SUCCINIC ACID, 15% PEG 3350, PH REMARK 280 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 27.66200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.26750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 55.69450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 66.26750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.66200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 55.69450 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -160.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A -2 REMARK 465 ASN A -1 REMARK 465 ALA A 0 REMARK 465 MET A 1 REMARK 465 GLY A 378 REMARK 465 ASN A 379 REMARK 465 ALA A 380 REMARK 465 VAL A 381 REMARK 465 SER B -2 REMARK 465 ASN B -1 REMARK 465 ALA B 0 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 465 GLU B 3 REMARK 465 THR B 4 REMARK 465 ALA B 377 REMARK 465 GLY B 378 REMARK 465 ASN B 379 REMARK 465 ALA B 380 REMARK 465 VAL B 381 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 ASP A 25 CG OD1 OD2 REMARK 470 ASP A 48 CG OD1 OD2 REMARK 470 LYS A 59 NZ REMARK 470 LYS A 170 CD CE NZ REMARK 470 LYS A 190 CD CE NZ REMARK 470 GLU A 317 CG CD OE1 OE2 REMARK 470 GLU B 8 CG CD OE1 OE2 REMARK 470 LYS B 28 CG CD CE NZ REMARK 470 LYS B 59 CG CD CE NZ REMARK 470 GLU B 78 CG CD OE1 OE2 REMARK 470 LYS B 79 CG CD CE NZ REMARK 470 ARG B 90 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 93 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 151 CG CD CE NZ REMARK 470 LYS B 170 CG CD CE NZ REMARK 470 LYS B 190 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 OG1 THR B 313 O HOH B 613 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 PRO A 76 107.87 -57.71 REMARK 500 MET A 102 34.43 -150.96 REMARK 500 ASP A 169 -80.86 -116.70 REMARK 500 PRO A 344 -169.59 -73.49 REMARK 500 LYS B 11 -33.98 -39.33 REMARK 500 PRO B 87 150.38 -49.82 REMARK 500 MET B 102 34.54 -150.32 REMARK 500 PRO B 344 -174.68 -69.90 REMARK 500 HIS B 350 19.09 59.61 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 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 68 NE2 REMARK 620 2 ASP A 101 OD1 100.9 REMARK 620 3 GLU A 164 OE1 140.7 98.1 REMARK 620 4 GLU A 164 OE2 87.7 147.0 59.0 REMARK 620 5 HOH A 609 O 105.1 110.7 99.7 97.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 68 NE2 REMARK 620 2 ASP B 101 OD1 97.0 REMARK 620 3 GLU B 164 OE2 143.1 89.4 REMARK 620 4 GLU B 164 OE1 93.7 139.8 60.7 REMARK 620 5 HOH B 547 O 113.8 101.7 100.2 109.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 101 OD2 REMARK 620 2 GLU B 136 OE2 76.5 REMARK 620 3 GLU B 136 OE1 127.5 51.1 REMARK 620 4 HIS B 350 NE2 94.9 95.9 89.5 REMARK 620 5 HOH B 547 O 79.9 78.9 90.4 173.4 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 404 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ISZ RELATED DB: PDB REMARK 900 RELATED ID: 1VGY RELATED DB: PDB REMARK 900 RELATED ID: IDP92725 RELATED DB: TARGETTRACK REMARK 900 RELATED ID: CSGID-IDP92725 RELATED DB: TARGETTRACK DBREF 4O23 A 1 381 UNP Q9JYL2 DAPE_NEIMB 1 381 DBREF 4O23 B 1 381 UNP Q9JYL2 DAPE_NEIMB 1 381 SEQADV 4O23 SER A -2 UNP Q9JYL2 EXPRESSION TAG SEQADV 4O23 ASN A -1 UNP Q9JYL2 EXPRESSION TAG SEQADV 4O23 ALA A 0 UNP Q9JYL2 EXPRESSION TAG SEQADV 4O23 SER B -2 UNP Q9JYL2 EXPRESSION TAG SEQADV 4O23 ASN B -1 UNP Q9JYL2 EXPRESSION TAG SEQADV 4O23 ALA B 0 UNP Q9JYL2 EXPRESSION TAG SEQRES 1 A 384 SER ASN ALA MET THR GLU THR GLN SER LEU GLU LEU ALA SEQRES 2 A 384 LYS GLU LEU ILE SER ARG PRO SER VAL THR PRO ASP ASP SEQRES 3 A 384 ARG ASP CYS GLN LYS LEU LEU ALA GLU ARG LEU HIS LYS SEQRES 4 A 384 ILE GLY PHE ALA ALA GLU GLU LEU HIS PHE GLY ASP THR SEQRES 5 A 384 LYS ASN ILE TRP LEU ARG ARG GLY THR LYS ALA PRO VAL SEQRES 6 A 384 VAL CYS PHE ALA GLY HIS THR ASP VAL VAL PRO THR GLY SEQRES 7 A 384 PRO VAL GLU LYS TRP ASP SER PRO PRO PHE GLU PRO ALA SEQRES 8 A 384 GLU ARG ASP GLY ARG LEU TYR GLY ARG GLY ALA ALA ASP SEQRES 9 A 384 MET LYS THR SER ILE ALA CYS PHE VAL THR ALA CYS GLU SEQRES 10 A 384 ARG PHE VAL ALA LYS HIS PRO ASN HIS GLN GLY SER ILE SEQRES 11 A 384 ALA LEU LEU ILE THR SER ASP GLU GLU GLY ASP ALA LEU SEQRES 12 A 384 ASP GLY THR THR LYS VAL VAL ASP VAL LEU LYS ALA ARG SEQRES 13 A 384 ASP GLU LEU ILE ASP TYR CYS ILE VAL GLY GLU PRO THR SEQRES 14 A 384 ALA VAL ASP LYS LEU GLY ASP MET ILE LYS ASN GLY ARG SEQRES 15 A 384 ARG GLY SER LEU SER GLY ASN LEU THR VAL LYS GLY LYS SEQRES 16 A 384 GLN GLY HIS ILE ALA TYR PRO HIS LEU ALA ILE ASN PRO SEQRES 17 A 384 VAL HIS THR PHE ALA PRO ALA LEU LEU GLU LEU THR GLN SEQRES 18 A 384 GLU VAL TRP ASP GLU GLY ASN GLU TYR PHE PRO PRO THR SEQRES 19 A 384 SER PHE GLN ILE SER ASN ILE ASN GLY GLY THR GLY ALA SEQRES 20 A 384 THR ASN VAL ILE PRO GLY GLU LEU ASN VAL LYS PHE ASN SEQRES 21 A 384 PHE ARG PHE SER THR GLU SER THR GLU ALA GLY LEU LYS SEQRES 22 A 384 GLN ARG VAL HIS ALA ILE LEU ASP LYS HIS GLY VAL GLN SEQRES 23 A 384 TYR ASP LEU GLN TRP SER CYS SER GLY GLN PRO PHE LEU SEQRES 24 A 384 THR GLN ALA GLY LYS LEU THR ASP VAL ALA ARG ALA ALA SEQRES 25 A 384 ILE ALA GLU THR CYS GLY ILE GLU ALA GLU LEU SER THR SEQRES 26 A 384 THR GLY GLY THR SER ASP GLY ARG PHE ILE LYS ALA ILE SEQRES 27 A 384 ALA GLN GLU LEU ILE GLU LEU GLY PRO SER ASN ALA THR SEQRES 28 A 384 ILE HIS GLN ILE ASN GLU ASN VAL ARG LEU ASN ASP ILE SEQRES 29 A 384 PRO LYS LEU SER ALA VAL TYR GLU GLY ILE LEU ALA ARG SEQRES 30 A 384 LEU LEU ALA GLY ASN ALA VAL SEQRES 1 B 384 SER ASN ALA MET THR GLU THR GLN SER LEU GLU LEU ALA SEQRES 2 B 384 LYS GLU LEU ILE SER ARG PRO SER VAL THR PRO ASP ASP SEQRES 3 B 384 ARG ASP CYS GLN LYS LEU LEU ALA GLU ARG LEU HIS LYS SEQRES 4 B 384 ILE GLY PHE ALA ALA GLU GLU LEU HIS PHE GLY ASP THR SEQRES 5 B 384 LYS ASN ILE TRP LEU ARG ARG GLY THR LYS ALA PRO VAL SEQRES 6 B 384 VAL CYS PHE ALA GLY HIS THR ASP VAL VAL PRO THR GLY SEQRES 7 B 384 PRO VAL GLU LYS TRP ASP SER PRO PRO PHE GLU PRO ALA SEQRES 8 B 384 GLU ARG ASP GLY ARG LEU TYR GLY ARG GLY ALA ALA ASP SEQRES 9 B 384 MET LYS THR SER ILE ALA CYS PHE VAL THR ALA CYS GLU SEQRES 10 B 384 ARG PHE VAL ALA LYS HIS PRO ASN HIS GLN GLY SER ILE SEQRES 11 B 384 ALA LEU LEU ILE THR SER ASP GLU GLU GLY ASP ALA LEU SEQRES 12 B 384 ASP GLY THR THR LYS VAL VAL ASP VAL LEU LYS ALA ARG SEQRES 13 B 384 ASP GLU LEU ILE ASP TYR CYS ILE VAL GLY GLU PRO THR SEQRES 14 B 384 ALA VAL ASP LYS LEU GLY ASP MET ILE LYS ASN GLY ARG SEQRES 15 B 384 ARG GLY SER LEU SER GLY ASN LEU THR VAL LYS GLY LYS SEQRES 16 B 384 GLN GLY HIS ILE ALA TYR PRO HIS LEU ALA ILE ASN PRO SEQRES 17 B 384 VAL HIS THR PHE ALA PRO ALA LEU LEU GLU LEU THR GLN SEQRES 18 B 384 GLU VAL TRP ASP GLU GLY ASN GLU TYR PHE PRO PRO THR SEQRES 19 B 384 SER PHE GLN ILE SER ASN ILE ASN GLY GLY THR GLY ALA SEQRES 20 B 384 THR ASN VAL ILE PRO GLY GLU LEU ASN VAL LYS PHE ASN SEQRES 21 B 384 PHE ARG PHE SER THR GLU SER THR GLU ALA GLY LEU LYS SEQRES 22 B 384 GLN ARG VAL HIS ALA ILE LEU ASP LYS HIS GLY VAL GLN SEQRES 23 B 384 TYR ASP LEU GLN TRP SER CYS SER GLY GLN PRO PHE LEU SEQRES 24 B 384 THR GLN ALA GLY LYS LEU THR ASP VAL ALA ARG ALA ALA SEQRES 25 B 384 ILE ALA GLU THR CYS GLY ILE GLU ALA GLU LEU SER THR SEQRES 26 B 384 THR GLY GLY THR SER ASP GLY ARG PHE ILE LYS ALA ILE SEQRES 27 B 384 ALA GLN GLU LEU ILE GLU LEU GLY PRO SER ASN ALA THR SEQRES 28 B 384 ILE HIS GLN ILE ASN GLU ASN VAL ARG LEU ASN ASP ILE SEQRES 29 B 384 PRO LYS LEU SER ALA VAL TYR GLU GLY ILE LEU ALA ARG SEQRES 30 B 384 LEU LEU ALA GLY ASN ALA VAL HET ZN A 401 1 HET ZN B 401 1 HET ZN B 402 1 HET SO4 B 403 5 HET SO4 B 404 5 HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION FORMUL 3 ZN 3(ZN 2+) FORMUL 6 SO4 2(O4 S 2-) FORMUL 8 HOH *380(H2 O) HELIX 1 1 THR A 4 SER A 15 1 12 HELIX 2 2 ASP A 25 HIS A 35 1 11 HELIX 3 3 LYS A 36 GLY A 38 5 3 HELIX 4 4 PRO A 76 TRP A 80 5 5 HELIX 5 5 MET A 102 HIS A 120 1 19 HELIX 6 6 GLY A 142 ARG A 153 1 12 HELIX 7 7 TYR A 198 ALA A 202 5 5 HELIX 8 8 ASN A 204 GLU A 219 1 16 HELIX 9 9 THR A 265 HIS A 280 1 16 HELIX 10 10 GLY A 300 GLY A 315 1 16 HELIX 11 11 ASP A 328 LYS A 333 1 6 HELIX 12 12 ASN A 359 ALA A 377 1 19 HELIX 13 13 SER B 6 SER B 15 1 10 HELIX 14 14 ASP B 25 LYS B 36 1 12 HELIX 15 15 MET B 102 HIS B 120 1 19 HELIX 16 16 GLY B 142 ALA B 152 1 11 HELIX 17 17 TYR B 198 ALA B 202 5 5 HELIX 18 18 ASN B 204 GLU B 219 1 16 HELIX 19 19 THR B 265 HIS B 280 1 16 HELIX 20 20 GLY B 300 CYS B 314 1 15 HELIX 21 21 ASP B 328 LYS B 333 1 6 HELIX 22 22 ASN B 359 LEU B 376 1 18 SHEET 1 A 6 ALA A 40 GLU A 43 0 SHEET 2 A 6 ASN A 51 ARG A 56 -1 O ARG A 55 N ALA A 40 SHEET 3 A 6 SER A 126 THR A 132 -1 O ILE A 127 N ARG A 56 SHEET 4 A 6 VAL A 62 HIS A 68 1 N VAL A 63 O SER A 126 SHEET 5 A 6 ILE A 157 VAL A 162 1 O ILE A 161 N CYS A 64 SHEET 6 A 6 ALA A 336 GLU A 341 1 O ILE A 340 N VAL A 162 SHEET 1 B 3 ALA A 88 ARG A 90 0 SHEET 2 B 3 ARG A 93 TYR A 95 -1 O ARG A 93 N ARG A 90 SHEET 3 B 3 ASN A 355 ARG A 357 -1 O VAL A 356 N LEU A 94 SHEET 1 C 2 MET A 174 LYS A 176 0 SHEET 2 C 2 GLU A 319 SER A 321 1 O GLU A 319 N ILE A 175 SHEET 1 D 2 GLY A 178 ARG A 179 0 SHEET 2 D 2 PHE A 295 LEU A 296 -1 O PHE A 295 N ARG A 179 SHEET 1 E 8 TYR A 284 GLY A 292 0 SHEET 2 E 8 GLY A 181 LYS A 190 -1 N ASN A 186 O GLN A 287 SHEET 3 E 8 GLU A 251 PHE A 260 -1 O VAL A 254 N LEU A 187 SHEET 4 E 8 SER A 232 GLY A 240 -1 N ASN A 239 O ASN A 253 SHEET 5 E 8 SER B 232 GLY B 240 -1 O ILE B 238 N GLY A 240 SHEET 6 E 8 GLU B 251 PHE B 260 -1 O LYS B 255 N ASN B 237 SHEET 7 E 8 GLY B 181 LYS B 190 -1 N LEU B 187 O VAL B 254 SHEET 8 E 8 TYR B 284 GLY B 292 -1 O SER B 289 N SER B 184 SHEET 1 F 2 GLY A 194 HIS A 195 0 SHEET 2 F 2 VAL A 247 ILE A 248 -1 O ILE A 248 N GLY A 194 SHEET 1 G 5 ASN B 51 ARG B 56 0 SHEET 2 G 5 SER B 126 THR B 132 -1 O LEU B 129 N LEU B 54 SHEET 3 G 5 VAL B 62 HIS B 68 1 N VAL B 63 O SER B 126 SHEET 4 G 5 ILE B 157 VAL B 162 1 O TYR B 159 N CYS B 64 SHEET 5 G 5 ALA B 336 GLU B 341 1 O ILE B 340 N VAL B 162 SHEET 1 H 3 ALA B 88 GLU B 89 0 SHEET 2 H 3 LEU B 94 TYR B 95 -1 O TYR B 95 N ALA B 88 SHEET 3 H 3 ASN B 355 VAL B 356 -1 O VAL B 356 N LEU B 94 SHEET 1 I 2 MET B 174 LYS B 176 0 SHEET 2 I 2 GLU B 319 SER B 321 1 O GLU B 319 N ILE B 175 SHEET 1 J 2 GLY B 178 ARG B 179 0 SHEET 2 J 2 PHE B 295 LEU B 296 -1 O PHE B 295 N ARG B 179 SHEET 1 K 2 GLY B 194 HIS B 195 0 SHEET 2 K 2 VAL B 247 ILE B 248 -1 O ILE B 248 N GLY B 194 LINK NE2 HIS A 68 ZN ZN A 401 1555 1555 2.12 LINK OD1 ASP A 101 ZN ZN A 401 1555 1555 1.99 LINK OE1 GLU A 164 ZN ZN A 401 1555 1555 2.11 LINK OE2 GLU A 164 ZN ZN A 401 1555 1555 2.32 LINK ZN ZN A 401 O HOH A 609 1555 1555 2.07 LINK NE2 HIS B 68 ZN ZN B 401 1555 1555 2.06 LINK OD1 ASP B 101 ZN ZN B 401 1555 1555 2.04 LINK OD2 ASP B 101 ZN ZN B 402 1555 1555 2.14 LINK OE2 GLU B 136 ZN ZN B 402 1555 1555 2.49 LINK OE1 GLU B 136 ZN ZN B 402 1555 1555 2.59 LINK OE2 GLU B 164 ZN ZN B 401 1555 1555 2.10 LINK OE1 GLU B 164 ZN ZN B 401 1555 1555 2.23 LINK NE2 HIS B 350 ZN ZN B 402 1555 1555 2.08 LINK ZN ZN B 401 O HOH B 547 1555 1555 2.07 LINK ZN ZN B 402 O HOH B 547 1555 1555 2.07 CISPEP 1 THR A 20 PRO A 21 0 -3.95 CISPEP 2 ALA A 60 PRO A 61 0 0.53 CISPEP 3 ASP A 101 MET A 102 0 0.59 CISPEP 4 THR B 20 PRO B 21 0 -1.41 CISPEP 5 ALA B 60 PRO B 61 0 -1.12 CISPEP 6 ASP B 101 MET B 102 0 -0.41 SITE 1 AC1 4 HIS A 68 ASP A 101 GLU A 164 HOH A 609 SITE 1 AC2 5 HIS B 68 ASP B 101 GLU B 135 GLU B 164 SITE 2 AC2 5 HOH B 547 SITE 1 AC3 4 ASP B 101 GLU B 136 HIS B 350 HOH B 547 SITE 1 AC4 5 HIS A 195 ASN A 246 ARG B 259 GLY B 325 SITE 2 AC4 5 THR B 326 SITE 1 AC5 4 ARG A 259 HOH A 562 HIS B 195 ASN B 246 CRYST1 55.324 111.389 132.535 90.00 90.00 90.00 P 21 21 21 8 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 0.018075 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008978 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007545 0.00000