HEADER HYDROLASE/DNA 03-AUG-12 4B5H TITLE SUBSTATE BOUND INACTIVE MUTANT OF NEISSERIA AP ENDONUCLEASE IN TITLE 2 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 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: 5'-D(*GP*CP*TP*AP*CP*3DRP*CP*AP*TP*CP*GP)-3'; COMPND 10 CHAIN: U; COMPND 11 SYNONYM: DNA 11MER CONTAINING ABASIC RESIDUE; COMPND 12 ENGINEERED: YES; COMPND 13 MUTATION: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: 5'-D(*CP*GP*AP*TP*GP*GP*GP*TP*AP*GP*CP)-3'; COMPND 16 CHAIN: V; COMPND 17 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 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 4B5H 1 REMARK LINK REVDAT 3 28-FEB-18 4B5H 1 JRNL REVDAT 2 31-OCT-12 4B5H 1 JRNL REVDAT 1 17-OCT-12 4B5H 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. 3.05 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) : 3.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 5920 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.295 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 582 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 31.0663 - 4.8371 0.97 1385 160 0.2017 0.3108 REMARK 3 2 4.8371 - 3.8417 0.99 1311 155 0.1592 0.2634 REMARK 3 3 3.8417 - 3.3567 1.00 1319 144 0.1773 0.3040 REMARK 3 4 3.3567 - 3.0501 1.00 1323 123 0.2134 0.3157 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 : 0.34 REMARK 3 B_SOL : 52.07 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.480 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.660 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) : 2.66490 REMARK 3 B22 (A**2) : 2.66490 REMARK 3 B33 (A**2) : -5.32980 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 2676 REMARK 3 ANGLE : 0.528 3626 REMARK 3 CHIRALITY : 0.034 375 REMARK 3 PLANARITY : 0.002 392 REMARK 3 DIHEDRAL : 16.574 977 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): -5.0873 21.6673 -13.5277 REMARK 3 T TENSOR REMARK 3 T11: 0.2354 T22: 0.2582 REMARK 3 T33: 0.1297 T12: 0.2251 REMARK 3 T13: 0.0105 T23: 0.0708 REMARK 3 L TENSOR REMARK 3 L11: 2.2796 L22: 1.3341 REMARK 3 L33: 0.8175 L12: 1.6543 REMARK 3 L13: -0.5921 L23: -0.1155 REMARK 3 S TENSOR REMARK 3 S11: 0.5307 S12: 0.3321 S13: 0.1015 REMARK 3 S21: -0.0049 S22: -0.3674 S23: -0.0792 REMARK 3 S31: -0.1357 S32: -0.0165 S33: 0.2701 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 71:85) REMARK 3 ORIGIN FOR THE GROUP (A): 1.8760 12.3756 -8.0892 REMARK 3 T TENSOR REMARK 3 T11: 0.3277 T22: 0.3804 REMARK 3 T33: 0.3115 T12: 0.3503 REMARK 3 T13: 0.2144 T23: -0.0037 REMARK 3 L TENSOR REMARK 3 L11: 2.7366 L22: 1.7323 REMARK 3 L33: 5.5264 L12: 1.9626 REMARK 3 L13: 2.1696 L23: 2.6641 REMARK 3 S TENSOR REMARK 3 S11: 0.3586 S12: 1.1888 S13: -0.0106 REMARK 3 S21: 0.7522 S22: 0.1367 S23: -0.0924 REMARK 3 S31: 1.1105 S32: 0.5855 S33: 1.3687 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 86:119) REMARK 3 ORIGIN FOR THE GROUP (A): -11.4437 9.4300 -7.8415 REMARK 3 T TENSOR REMARK 3 T11: 0.3761 T22: 0.1371 REMARK 3 T33: 0.2585 T12: -0.0271 REMARK 3 T13: -0.0620 T23: -0.1120 REMARK 3 L TENSOR REMARK 3 L11: 2.0161 L22: 0.7273 REMARK 3 L33: 0.7217 L12: -0.2317 REMARK 3 L13: -0.5317 L23: -0.4876 REMARK 3 S TENSOR REMARK 3 S11: -0.4488 S12: 0.0955 S13: 0.0313 REMARK 3 S21: 0.0553 S22: -0.0101 S23: 0.1522 REMARK 3 S31: 0.3014 S32: -0.0534 S33: -2.2063 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 120:136) REMARK 3 ORIGIN FOR THE GROUP (A): -17.5196 3.9910 -1.9868 REMARK 3 T TENSOR REMARK 3 T11: 0.6426 T22: 0.0574 REMARK 3 T33: 0.3537 T12: -0.1974 REMARK 3 T13: -0.1002 T23: -0.1596 REMARK 3 L TENSOR REMARK 3 L11: 3.4902 L22: 2.7700 REMARK 3 L33: 2.1601 L12: -0.6235 REMARK 3 L13: 1.8761 L23: -2.0833 REMARK 3 S TENSOR REMARK 3 S11: 0.4920 S12: 0.0696 S13: -0.4111 REMARK 3 S21: -0.0329 S22: -0.1504 S23: -1.2675 REMARK 3 S31: 1.1529 S32: -0.2146 S33: -0.1842 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 137:142) REMARK 3 ORIGIN FOR THE GROUP (A): -1.8925 5.2425 5.9821 REMARK 3 T TENSOR REMARK 3 T11: 0.8731 T22: 0.4670 REMARK 3 T33: 0.6236 T12: -0.2389 REMARK 3 T13: -0.3843 T23: -0.0004 REMARK 3 L TENSOR REMARK 3 L11: 0.0296 L22: 0.0102 REMARK 3 L33: 0.0185 L12: -0.0087 REMARK 3 L13: -0.0026 L23: -0.0114 REMARK 3 S TENSOR REMARK 3 S11: 0.2455 S12: 0.0399 S13: 0.3983 REMARK 3 S21: -0.4580 S22: -0.9090 S23: 0.6702 REMARK 3 S31: -0.3956 S32: 0.1372 S33: -0.0001 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN A AND RESID 143:196) REMARK 3 ORIGIN FOR THE GROUP (A): -19.5583 16.3881 5.0482 REMARK 3 T TENSOR REMARK 3 T11: 0.1009 T22: 0.3348 REMARK 3 T33: 0.2276 T12: 0.0158 REMARK 3 T13: 0.0406 T23: -0.0433 REMARK 3 L TENSOR REMARK 3 L11: 1.1560 L22: 0.9285 REMARK 3 L33: 1.7038 L12: 0.0578 REMARK 3 L13: 0.7003 L23: 0.1804 REMARK 3 S TENSOR REMARK 3 S11: 0.0840 S12: -0.5086 S13: 0.0096 REMARK 3 S21: 0.2664 S22: -0.2654 S23: -0.1098 REMARK 3 S31: -0.1874 S32: -0.7676 S33: 0.0008 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN A AND RESID 197:256) REMARK 3 ORIGIN FOR THE GROUP (A): -13.7442 25.9544 0.5414 REMARK 3 T TENSOR REMARK 3 T11: 0.3471 T22: 0.0594 REMARK 3 T33: 0.1971 T12: -0.0157 REMARK 3 T13: 0.0605 T23: -0.0485 REMARK 3 L TENSOR REMARK 3 L11: 1.3278 L22: 1.0133 REMARK 3 L33: 2.2594 L12: 0.0175 REMARK 3 L13: 0.3291 L23: -1.0088 REMARK 3 S TENSOR REMARK 3 S11: 0.1895 S12: -0.1809 S13: 0.2235 REMARK 3 S21: -0.2813 S22: 0.0376 S23: 0.4993 REMARK 3 S31: -0.1359 S32: -0.5475 S33: 0.1615 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN U AND RESID 31:35) REMARK 3 ORIGIN FOR THE GROUP (A): -25.4934 16.9662 -22.4531 REMARK 3 T TENSOR REMARK 3 T11: 0.7184 T22: 1.1667 REMARK 3 T33: 0.3460 T12: -0.0807 REMARK 3 T13: -0.1210 T23: -0.0685 REMARK 3 L TENSOR REMARK 3 L11: 0.9993 L22: 0.1896 REMARK 3 L33: 1.0032 L12: 0.3152 REMARK 3 L13: -0.7604 L23: -0.0580 REMARK 3 S TENSOR REMARK 3 S11: 0.2953 S12: 2.5795 S13: 0.2079 REMARK 3 S21: -0.8748 S22: 1.6536 S23: -0.8215 REMARK 3 S31: -0.0446 S32: -0.2013 S33: 0.0711 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN U AND RESID 36:41) REMARK 3 ORIGIN FOR THE GROUP (A): -35.5593 26.5810 -5.8137 REMARK 3 T TENSOR REMARK 3 T11: 0.6929 T22: 1.7414 REMARK 3 T33: 0.9104 T12: 0.4615 REMARK 3 T13: -0.1512 T23: 0.3910 REMARK 3 L TENSOR REMARK 3 L11: 0.0321 L22: 0.0589 REMARK 3 L33: 0.0084 L12: -0.0366 REMARK 3 L13: -0.0080 L23: 0.0088 REMARK 3 S TENSOR REMARK 3 S11: 0.2703 S12: 0.0563 S13: 0.8455 REMARK 3 S21: -0.1117 S22: 1.0363 S23: 0.5579 REMARK 3 S31: 0.9615 S32: -1.1841 S33: 0.0005 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: (CHAIN V AND RESID 42:46) REMARK 3 ORIGIN FOR THE GROUP (A): -42.2783 21.8241 -6.7167 REMARK 3 T TENSOR REMARK 3 T11: 3.5354 T22: 2.9487 REMARK 3 T33: 1.0653 T12: -0.0708 REMARK 3 T13: 0.0459 T23: -0.0551 REMARK 3 L TENSOR REMARK 3 L11: 0.0027 L22: 0.0279 REMARK 3 L33: 0.0594 L12: -0.0091 REMARK 3 L13: -0.0136 L23: 0.0407 REMARK 3 S TENSOR REMARK 3 S11: 0.5055 S12: -0.0194 S13: 0.2950 REMARK 3 S21: 0.1515 S22: -0.1578 S23: -0.3617 REMARK 3 S31: -0.1715 S32: -0.2802 S33: 0.0000 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: (CHAIN V AND RESID 47:52) REMARK 3 ORIGIN FOR THE GROUP (A): -22.9457 24.3602 -20.1619 REMARK 3 T TENSOR REMARK 3 T11: 0.5193 T22: 1.1013 REMARK 3 T33: 0.4620 T12: 0.6225 REMARK 3 T13: -0.0471 T23: -0.0496 REMARK 3 L TENSOR REMARK 3 L11: 2.0076 L22: 0.7220 REMARK 3 L33: 2.0352 L12: -0.1615 REMARK 3 L13: -0.2147 L23: 0.0273 REMARK 3 S TENSOR REMARK 3 S11: -0.7358 S12: 1.0376 S13: 0.0191 REMARK 3 S21: 0.7499 S22: 0.3321 S23: 0.4505 REMARK 3 S31: -1.3385 S32: -1.2890 S33: 0.0033 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 4B5H 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_1290053622. 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 : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.8137 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5920 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 59.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.800 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.10000 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 (%): 37.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 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 60.48400 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 34.45350 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 34.45350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 90.72600 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 34.45350 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 34.45350 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 30.24200 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 34.45350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.45350 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 90.72600 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 34.45350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.45350 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 30.24200 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 60.48400 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.4 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, U, V 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ALA 29 TO THR REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ASP 149 TO ASN 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 ARG A 64 NE CZ NH1 NH2 REMARK 470 ARG A 75 NE CZ NH1 NH2 REMARK 470 GLU A 87 CD OE1 OE2 REMARK 470 LYS A 167 CD CE NZ REMARK 470 GLU A 177 CD OE1 OE2 REMARK 470 LYS A 181 CE NZ REMARK 470 LYS A 185 CD CE NZ REMARK 470 GLU A 259 O CD OE1 OE2 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 69.25 63.76 REMARK 500 ALA A 39 -175.35 -173.00 REMARK 500 SER A 67 -157.54 51.78 REMARK 500 ASN A 165 15.23 -147.33 REMARK 500 PHE A 171 24.06 -140.58 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 A1260 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 10 OD1 REMARK 620 2 GLU A 36 OE1 72.5 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 1260 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) ENDONUCLEASE IN PRESENCE OF METAL IONS REMARK 900 RELATED ID: 4B5I RELATED DB: PDB REMARK 900 PRODUCT COMPLEX OF NEISSERIA AP ENDONUCLEASE IN PRESENCE OF METAL REMARK 900 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 4B5H A 1 259 UNP C9X331 C9X331_NEIM8 1 259 DBREF 4B5H U 31 41 PDB 4B5H 4B5H 31 41 DBREF 4B5H V 42 52 PDB 4B5H 4B5H 42 52 SEQADV 4B5H THR A 29 UNP C9X331 ALA 29 ENGINEERED MUTATION SEQADV 4B5H GLY A 101 UNP C9X331 ASP 101 CONFLICT SEQADV 4B5H ASN A 149 UNP C9X331 ASP 149 ENGINEERED MUTATION 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 THR 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 ASN 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 11 DG DC DT DA DC 3DR DC DA DT DC DG SEQRES 1 V 11 DC DG DA DT DG DG DG DT DA DG DC HET 3DR U 36 11 HET MN A1260 1 HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETNAM MN MANGANESE (II) ION HETSYN 3DR ABASIC DIDEOXYRIBOSE FORMUL 2 3DR C5 H11 O6 P FORMUL 4 MN MN 2+ 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 ASN A 50 MET A 54 5 5 HELIX 4 4 ILE A 86 ARG A 91 1 6 HELIX 5 5 ALA A 116 ASN A 139 1 24 HELIX 6 6 GLN A 155 ASP A 158 5 4 HELIX 7 7 ASN A 161 ASN A 165 5 5 HELIX 8 8 LEU A 172 HIS A 184 1 13 HELIX 9 9 MET A 191 TYR A 196 1 6 HELIX 10 10 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 ASN 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 LINK O3' DC U 35 P 3DR U 36 1555 1555 1.61 LINK O3' 3DR U 36 P DC U 37 1555 1555 1.61 LINK OD1 ASN A 10 MN MN A1260 1555 1555 2.48 LINK OE1 GLU A 36 MN MN A1260 1555 1555 2.51 SITE 1 AC1 3 ASN A 10 GLU A 36 3DR U 36 CRYST1 68.907 68.907 120.968 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 0.014512 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014512 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008267 0.00000