HEADER HYDROLASE/DNA 03-AUG-12 4B5I TITLE PRODUCT COMPLEX OF NEISSERIA AP ENDONUCLEASE IN PRESENCE OF METAL IONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE EXODEOXYRIBONUCLEASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NEISSERIA AP ENDONUCLEASE; COMPND 5 EC: 3.1.11.2; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-D(*GP*CP*TP*AP*CP)-3'; COMPND 9 CHAIN: U; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: 5'-D(*CP*GP*AP*TP*GP*GP*GP*TP*AP*GP*CP)-3'; COMPND 13 CHAIN: V; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: 5'-D(*3DRP*CP*AP*TP*CP*GP)-3'; COMPND 17 CHAIN: X; COMPND 18 SYNONYM: DNA 6MER CONTAINING ABASIC RESIDUE; COMPND 19 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEISSERIA MENINGITIDIS; SOURCE 3 ORGANISM_TAXID: 487; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: NEISSERIA MENINGITIDIS; SOURCE 9 ORGANISM_TAXID: 487; SOURCE 10 MOL_ID: 3; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: NEISSERIA MENINGITIDIS; SOURCE 13 ORGANISM_TAXID: 487; SOURCE 14 MOL_ID: 4; SOURCE 15 SYNTHETIC: YES; SOURCE 16 ORGANISM_SCIENTIFIC: NEISSERIA MENINGITIDIS; SOURCE 17 ORGANISM_TAXID: 487 KEYWDS HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.LU,J.SILHAN,J.T.MACDONALD,E.P.CARPENTER,K.JENSEN,C.M.TANG, AUTHOR 2 G.S.BALDWIN,P.S.FREEMONT REVDAT 4 08-MAY-24 4B5I 1 REMARK LINK REVDAT 3 28-FEB-18 4B5I 1 JRNL REVDAT 2 31-OCT-12 4B5I 1 JRNL REVDAT 1 17-OCT-12 4B5I 0 JRNL AUTH D.LU,J.SILHAN,J.T.MACDONALD,E.P.CARPENTER,K.JENSEN,C.M.TANG, JRNL AUTH 2 G.S.BALDWIN,P.S.FREEMONT JRNL TITL STRUCTURAL BASIS FOR THE RECOGNITION AND CLEAVAGE OF ABASIC JRNL TITL 2 DNA IN NEISSERIA MENINGITIDIS. JRNL REF PROC. NATL. ACAD. SCI. V. 109 16852 2012 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 23035246 JRNL DOI 10.1073/PNAS.1206563109 REMARK 2 REMARK 2 RESOLUTION. 2.56 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 2.56 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.23 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 3 NUMBER OF REFLECTIONS : 9098 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 448 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 45.2377 - 3.6842 0.98 3218 161 0.1790 0.2100 REMARK 3 2 3.6842 - 2.9244 0.93 2894 156 0.2161 0.2872 REMARK 3 3 2.9244 - 2.5548 0.83 2538 131 0.2997 0.3701 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 : 0.32 REMARK 3 B_SOL : 37.21 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.860 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) : 2.41790 REMARK 3 B22 (A**2) : 2.41790 REMARK 3 B33 (A**2) : -4.83590 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 2683 REMARK 3 ANGLE : 0.536 3627 REMARK 3 CHIRALITY : 0.035 371 REMARK 3 PLANARITY : 0.001 393 REMARK 3 DIHEDRAL : 16.366 987 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 11 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 1:70) REMARK 3 ORIGIN FOR THE GROUP (A): -13.4889 29.1915 14.2242 REMARK 3 T TENSOR REMARK 3 T11: 0.2822 T22: 0.3077 REMARK 3 T33: 0.1131 T12: 0.1041 REMARK 3 T13: -0.0600 T23: -0.0733 REMARK 3 L TENSOR REMARK 3 L11: 1.5170 L22: 2.9216 REMARK 3 L33: 1.3782 L12: -1.4469 REMARK 3 L13: -0.3893 L23: 1.1930 REMARK 3 S TENSOR REMARK 3 S11: -0.4045 S12: -0.4548 S13: 0.2783 REMARK 3 S21: 0.7962 S22: 0.5422 S23: -0.1919 REMARK 3 S31: 0.0752 S32: -0.1413 S33: 0.0524 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 71:85) REMARK 3 ORIGIN FOR THE GROUP (A): -21.8563 37.0527 8.0559 REMARK 3 T TENSOR REMARK 3 T11: 0.3465 T22: 0.3605 REMARK 3 T33: 0.4093 T12: 0.1351 REMARK 3 T13: 0.0146 T23: 0.0109 REMARK 3 L TENSOR REMARK 3 L11: 0.2950 L22: 0.5076 REMARK 3 L33: 0.1889 L12: -0.3889 REMARK 3 L13: -0.1874 L23: 0.1643 REMARK 3 S TENSOR REMARK 3 S11: -0.2017 S12: -0.4670 S13: -0.4742 REMARK 3 S21: 0.2581 S22: -0.0788 S23: 0.1421 REMARK 3 S31: -0.4416 S32: -0.3748 S33: 0.0001 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 86:119) REMARK 3 ORIGIN FOR THE GROUP (A): -25.6829 23.5509 8.1398 REMARK 3 T TENSOR REMARK 3 T11: 0.0455 T22: 0.3041 REMARK 3 T33: 0.1328 T12: 0.0014 REMARK 3 T13: 0.1486 T23: 0.0346 REMARK 3 L TENSOR REMARK 3 L11: 2.0593 L22: 1.2718 REMARK 3 L33: 1.7643 L12: -0.0414 REMARK 3 L13: 0.5502 L23: 1.0261 REMARK 3 S TENSOR REMARK 3 S11: -0.3194 S12: -0.3924 S13: -0.0683 REMARK 3 S21: 0.0176 S22: -0.2282 S23: 0.1855 REMARK 3 S31: -0.0421 S32: -0.4349 S33: -0.6748 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 120:136) REMARK 3 ORIGIN FOR THE GROUP (A): -31.0458 17.8872 2.0998 REMARK 3 T TENSOR REMARK 3 T11: 0.1791 T22: 0.2835 REMARK 3 T33: 0.4941 T12: -0.0849 REMARK 3 T13: 0.0265 T23: -0.0566 REMARK 3 L TENSOR REMARK 3 L11: 0.2223 L22: 0.4292 REMARK 3 L33: 3.0281 L12: -0.0904 REMARK 3 L13: -0.2631 L23: 1.1305 REMARK 3 S TENSOR REMARK 3 S11: -0.1320 S12: 0.0978 S13: 0.1145 REMARK 3 S21: 0.2373 S22: 0.0360 S23: 0.3243 REMARK 3 S31: 0.8270 S32: -0.2615 S33: -0.0168 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 137:142) REMARK 3 ORIGIN FOR THE GROUP (A): -28.9139 33.3065 -5.7231 REMARK 3 T TENSOR REMARK 3 T11: 0.1245 T22: 0.4311 REMARK 3 T33: 0.3560 T12: 0.0162 REMARK 3 T13: -0.2071 T23: -0.0947 REMARK 3 L TENSOR REMARK 3 L11: 1.0469 L22: 1.8183 REMARK 3 L33: 3.6570 L12: 1.3158 REMARK 3 L13: -0.6418 L23: -0.0786 REMARK 3 S TENSOR REMARK 3 S11: 0.7060 S12: -0.2861 S13: -0.7002 REMARK 3 S21: -0.1490 S22: -0.2934 S23: 0.4528 REMARK 3 S31: 0.0356 S32: -0.0227 S33: 0.1846 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN A AND RESID 143:196) REMARK 3 ORIGIN FOR THE GROUP (A): -18.9941 15.1237 -4.6916 REMARK 3 T TENSOR REMARK 3 T11: 0.3420 T22: 0.2141 REMARK 3 T33: 0.2898 T12: 0.0043 REMARK 3 T13: -0.0269 T23: -0.0349 REMARK 3 L TENSOR REMARK 3 L11: 1.1846 L22: 1.9110 REMARK 3 L33: 1.6040 L12: 0.0453 REMARK 3 L13: -0.3329 L23: -0.2359 REMARK 3 S TENSOR REMARK 3 S11: -0.1167 S12: 0.1713 S13: -0.5277 REMARK 3 S21: -0.7471 S22: 0.0838 S23: 0.5124 REMARK 3 S31: 0.6665 S32: -0.3535 S33: 0.0006 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN A AND RESID 197:256) REMARK 3 ORIGIN FOR THE GROUP (A): -9.1240 20.5485 0.1825 REMARK 3 T TENSOR REMARK 3 T11: 0.1245 T22: 0.2731 REMARK 3 T33: 0.2406 T12: 0.0701 REMARK 3 T13: -0.0435 T23: -0.0888 REMARK 3 L TENSOR REMARK 3 L11: 0.5965 L22: 4.7540 REMARK 3 L33: 1.9290 L12: -0.6561 REMARK 3 L13: -0.7686 L23: 1.0186 REMARK 3 S TENSOR REMARK 3 S11: -0.2160 S12: -0.0270 S13: -0.2011 REMARK 3 S21: -0.1861 S22: 0.5648 S23: -0.5320 REMARK 3 S31: 0.3097 S32: 0.0827 S33: 0.1967 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN U AND RESID 31:35) REMARK 3 ORIGIN FOR THE GROUP (A): -18.8886 9.2359 22.9656 REMARK 3 T TENSOR REMARK 3 T11: 1.2308 T22: 0.6506 REMARK 3 T33: 0.8651 T12: -0.1127 REMARK 3 T13: 0.3704 T23: 0.0896 REMARK 3 L TENSOR REMARK 3 L11: 0.0496 L22: 0.0413 REMARK 3 L33: -0.0006 L12: -0.0459 REMARK 3 L13: 0.0031 L23: -0.0007 REMARK 3 S TENSOR REMARK 3 S11: 0.1516 S12: 1.4777 S13: 0.2202 REMARK 3 S21: 0.5065 S22: 0.5780 S23: -0.1415 REMARK 3 S31: 0.6407 S32: -0.2818 S33: 0.0020 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN V AND RESID 42:46) REMARK 3 ORIGIN FOR THE GROUP (A): -14.1052 -7.7495 6.8885 REMARK 3 T TENSOR REMARK 3 T11: 0.8918 T22: 1.2329 REMARK 3 T33: 1.0189 T12: 0.1077 REMARK 3 T13: 0.0870 T23: 0.6312 REMARK 3 L TENSOR REMARK 3 L11: 0.0616 L22: 0.0629 REMARK 3 L33: 0.0152 L12: -0.0646 REMARK 3 L13: -0.0064 L23: -0.0019 REMARK 3 S TENSOR REMARK 3 S11: 0.4130 S12: 0.5403 S13: -0.6861 REMARK 3 S21: -0.1155 S22: 0.0529 S23: 0.1906 REMARK 3 S31: 0.3295 S32: -0.2236 S33: 0.0016 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: (CHAIN V AND RESID 47:52) REMARK 3 ORIGIN FOR THE GROUP (A): -11.5310 11.2620 20.6194 REMARK 3 T TENSOR REMARK 3 T11: 0.8654 T22: 0.7224 REMARK 3 T33: 0.6601 T12: 0.3377 REMARK 3 T13: 0.0032 T23: -0.2358 REMARK 3 L TENSOR REMARK 3 L11: 0.2630 L22: 0.1366 REMARK 3 L33: 0.0198 L12: 0.1964 REMARK 3 L13: -0.0774 L23: -0.0578 REMARK 3 S TENSOR REMARK 3 S11: 0.3052 S12: -0.6113 S13: -1.2532 REMARK 3 S21: 0.9066 S22: -0.6885 S23: 0.3011 REMARK 3 S31: -0.2996 S32: -0.0313 S33: 0.0012 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: (CHAIN X AND RESID 36:41) REMARK 3 ORIGIN FOR THE GROUP (A): -9.7163 -1.0349 6.2878 REMARK 3 T TENSOR REMARK 3 T11: 0.9054 T22: 0.5113 REMARK 3 T33: 0.7564 T12: 0.2610 REMARK 3 T13: -0.0676 T23: -0.0027 REMARK 3 L TENSOR REMARK 3 L11: 0.5031 L22: 0.2145 REMARK 3 L33: 0.3190 L12: 0.2903 REMARK 3 L13: 0.1247 L23: -0.0630 REMARK 3 S TENSOR REMARK 3 S11: 0.3411 S12: -0.2499 S13: -0.4939 REMARK 3 S21: 0.0980 S22: -0.2982 S23: -0.6108 REMARK 3 S31: 0.2172 S32: 0.3943 S33: -0.0006 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 4B5I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1290053625. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9797 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9098 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550 REMARK 200 RESOLUTION RANGE LOW (A) : 59.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.200 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.83500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 34.54500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 34.54500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 89.75250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 34.54500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 34.54500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 29.91750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 34.54500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.54500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 89.75250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 34.54500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.54500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 29.91750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 59.83500 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.5 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, U, V, X 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 ALA A 257 REMARK 465 ALA A 258 REMARK 465 GLU A 259 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 GLU A 36 64.60 60.56 REMARK 500 SER A 67 -150.06 52.30 REMARK 500 PHE A 171 32.10 -141.51 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 MN A1257 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 36 OE2 REMARK 620 2 GLU A 36 OE1 50.4 REMARK 620 3 DC U 35 O3' 64.7 105.0 REMARK 620 4 3DR X 36 OP1 84.4 130.7 61.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 1257 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4B5F RELATED DB: PDB REMARK 900 SUBSTRATE BOUND NEISSERIA AP ENDONUCLEASE IN ABSENCE OF METAL IONS REMARK 900 (CRYSTAL FORM 1) REMARK 900 RELATED ID: 4B5G RELATED DB: PDB REMARK 900 SUBSTRATE BOUND NEISSERIA AP ENDONUCLEASE IN ABSENCE OF METAL IONS REMARK 900 (CRYSTAL FORM 2) REMARK 900 RELATED ID: 4B5H RELATED DB: PDB REMARK 900 SUBSTATE BOUND INACTIVE MUTANT OF NEISSERIA AP ENDONUCLEASE IN REMARK 900 PRESENCE OF METAL IONS REMARK 900 RELATED ID: 4B5J RELATED DB: PDB REMARK 900 NEISSERIA AP ENDONUCLEASE BOUND TO THE SUBSTRATE WITH AN ORPHAN REMARK 900 ADENINE BASE REMARK 900 RELATED ID: 4B5M RELATED DB: PDB REMARK 900 NEISSERIA AP ENDONUCLEASE BOUND TO THE SUBSTRATE WITH A CYTOSINE REMARK 900 ORPHAN BASE DBREF 4B5I A 1 259 UNP C9X331 C9X331_NEIM8 1 259 DBREF 4B5I U 31 35 PDB 4B5I 4B5I 31 35 DBREF 4B5I V 42 52 PDB 4B5I 4B5I 42 52 DBREF 4B5I X 36 41 PDB 4B5I 4B5I 36 41 SEQADV 4B5I GLY A 101 UNP C9X331 ASP 101 CONFLICT SEQRES 1 A 259 MET LEU LYS ILE ILE SER ALA ASN VAL ASN GLY ILE ARG SEQRES 2 A 259 SER ALA TYR LYS LYS GLY PHE TYR GLU TYR ILE ALA ALA SEQRES 3 A 259 SER GLY ALA ASP ILE VAL CYS VAL GLN GLU LEU LYS ALA SEQRES 4 A 259 GLN GLU ALA ASP LEU SER ALA ASP MET LYS ASN PRO HIS SEQRES 5 A 259 GLY MET HIS GLY HIS TRP HIS CYS ALA GLU LYS ARG GLY SEQRES 6 A 259 TYR SER GLY VAL ALA VAL TYR SER LYS ARG LYS PRO ASP SEQRES 7 A 259 ASN VAL GLN ILE GLY MET GLY ILE GLU GLU PHE ASP ARG SEQRES 8 A 259 GLU GLY ARG PHE VAL ARG CYS ASP PHE GLY ARG LEU SER SEQRES 9 A 259 VAL ILE SER LEU TYR LEU PRO SER GLY SER SER ALA GLU SEQRES 10 A 259 GLU ARG GLN GLN VAL LYS TYR ARG PHE LEU ASP ALA PHE SEQRES 11 A 259 TYR PRO MET LEU GLU ALA MET LYS ASN GLU GLY ARG ASP SEQRES 12 A 259 ILE VAL VAL CYS GLY ASP TRP ASN ILE ALA HIS GLN ASN SEQRES 13 A 259 ILE ASP LEU LYS ASN TRP LYS GLY ASN GLN LYS ASN SER SEQRES 14 A 259 GLY PHE LEU PRO GLU GLU ARG GLU TRP ILE GLY LYS VAL SEQRES 15 A 259 ILE HIS LYS LEU GLY TRP THR ASP MET TRP ARG THR LEU SEQRES 16 A 259 TYR PRO ASP VAL PRO GLY TYR THR TRP TRP SER ASN ARG SEQRES 17 A 259 GLY GLN ALA TYR ALA LYS ASP VAL GLY TRP ARG ILE ASP SEQRES 18 A 259 TYR GLN MET VAL THR PRO GLU LEU ALA ALA LYS ALA VAL SEQRES 19 A 259 SER ALA HIS VAL TYR LYS ASP GLU LYS PHE SER ASP HIS SEQRES 20 A 259 ALA PRO LEU VAL VAL GLU TYR ASP TYR ALA ALA GLU SEQRES 1 U 5 DG DC DT DA DC SEQRES 1 V 11 DC DG DA DT DG DG DG DT DA DG DC SEQRES 1 X 6 3DR DC DA DT DC DG HET 3DR X 36 12 HET MN A1257 1 HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETNAM MN MANGANESE (II) ION HETSYN 3DR ABASIC DIDEOXYRIBOSE FORMUL 4 3DR C5 H11 O6 P FORMUL 5 MN MN 2+ FORMUL 6 HOH *32(H2 O) HELIX 1 1 GLY A 11 LYS A 18 1 8 HELIX 2 2 GLY A 19 SER A 27 1 9 HELIX 3 3 SER A 45 ASN A 50 1 6 HELIX 4 4 PRO A 51 MET A 54 5 4 HELIX 5 5 ILE A 86 ARG A 91 1 6 HELIX 6 6 ALA A 116 GLU A 140 1 25 HELIX 7 7 GLN A 155 ASP A 158 5 4 HELIX 8 8 LEU A 172 LYS A 185 1 14 HELIX 9 9 MET A 191 TYR A 196 1 6 HELIX 10 10 GLN A 210 ASP A 215 1 6 HELIX 11 11 THR A 226 ALA A 231 1 6 SHEET 1 AA 6 HIS A 55 HIS A 59 0 SHEET 2 AA 6 VAL A 69 SER A 73 -1 O VAL A 69 N HIS A 59 SHEET 3 AA 6 ILE A 31 GLN A 35 -1 O VAL A 32 N TYR A 72 SHEET 4 AA 6 LEU A 2 ASN A 8 1 O ILE A 5 N CYS A 33 SHEET 5 AA 6 LEU A 250 TYR A 254 -1 O LEU A 250 N SER A 6 SHEET 6 AA 6 ALA A 233 VAL A 238 -1 N VAL A 234 O GLU A 253 SHEET 1 AB 6 ASN A 79 ILE A 82 0 SHEET 2 AB 6 PHE A 95 PHE A 100 -1 O ARG A 97 N GLN A 81 SHEET 3 AB 6 LEU A 103 TYR A 109 -1 O LEU A 103 N PHE A 100 SHEET 4 AB 6 ASP A 143 ASP A 149 1 O ASP A 143 N SER A 104 SHEET 5 AB 6 ASP A 221 VAL A 225 -1 O TYR A 222 N GLY A 148 SHEET 6 AB 6 THR A 189 ASP A 190 -1 O THR A 189 N VAL A 225 SHEET 1 AC 2 TRP A 204 TRP A 205 0 SHEET 2 AC 2 GLY A 217 TRP A 218 -1 N TRP A 218 O TRP A 204 LINK O3' 3DR X 36 P DC X 37 1555 1555 1.61 LINK OE2 GLU A 36 MN MN A1257 1555 1555 2.52 LINK OE1 GLU A 36 MN MN A1257 1555 1555 2.63 LINK MN MN A1257 O3' DC U 35 1555 1555 2.57 LINK MN MN A1257 OP1 3DR X 36 1555 1555 2.54 SITE 1 AC1 4 GLU A 36 ASP A 246 DC U 35 3DR X 36 CRYST1 69.090 69.090 119.670 90.00 90.00 90.00 P 43 21 2 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 0.014474 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014474 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008356 0.00000