HEADER HYDROLASE/DNA 03-AUG-12 4B5J TITLE NEISSERIA AP ENDONUCLEASE BOUND TO THE SUBSTRATE WITH AN ORPHAN TITLE 2 ADENINE BASE 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*(3DR)P*CP*AP*TP*CP*GP)-3'; COMPND 9 CHAIN: U; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: 5'-D(*CP*GP*AP*TP*GP*AP*GP*TP*AP*GP*CP)-3'; COMPND 13 CHAIN: V; COMPND 14 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 4B5J 1 LINK REVDAT 3 28-FEB-18 4B5J 1 JRNL REVDAT 2 31-OCT-12 4B5J 1 JRNL REVDAT 1 17-OCT-12 4B5J 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. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 18120 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) : 0.208 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.380 REMARK 3 FREE R VALUE TEST SET COUNT : 1862 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 27.8288 - 4.5188 0.97 1748 193 0.1621 0.2120 REMARK 3 2 4.5188 - 3.5891 1.00 1680 194 0.1654 0.2044 REMARK 3 3 3.5891 - 3.1361 1.00 1670 162 0.2138 0.2300 REMARK 3 4 3.1361 - 2.8497 0.99 1650 181 0.2331 0.3207 REMARK 3 5 2.8497 - 2.6456 1.00 1595 219 0.2549 0.3160 REMARK 3 6 2.6456 - 2.4897 1.00 1629 173 0.2845 0.3370 REMARK 3 7 2.4897 - 2.3651 1.00 1614 181 0.3034 0.3755 REMARK 3 8 2.3651 - 2.2622 0.99 1604 181 0.2920 0.4029 REMARK 3 9 2.2622 - 2.1752 0.98 1563 196 0.2686 0.3436 REMARK 3 10 2.1752 - 2.1001 0.94 1505 182 0.2875 0.3267 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.83 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 48.66 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.390 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.410 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) : 3.12820 REMARK 3 B22 (A**2) : 3.12820 REMARK 3 B33 (A**2) : -6.25650 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 : 0.006 2692 REMARK 3 ANGLE : 0.761 3639 REMARK 3 CHIRALITY : 0.050 372 REMARK 3 PLANARITY : 0.002 395 REMARK 3 DIHEDRAL : 17.790 997 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): 22.1564 -4.9107 14.0138 REMARK 3 T TENSOR REMARK 3 T11: 0.3157 T22: 0.3181 REMARK 3 T33: 0.2616 T12: 0.0781 REMARK 3 T13: -0.0285 T23: -0.0140 REMARK 3 L TENSOR REMARK 3 L11: 0.4256 L22: 1.1623 REMARK 3 L33: 1.6344 L12: -0.3594 REMARK 3 L13: -0.0919 L23: 1.3222 REMARK 3 S TENSOR REMARK 3 S11: -0.3213 S12: -0.1777 S13: -0.0302 REMARK 3 S21: 0.1640 S22: 0.2579 S23: -0.1536 REMARK 3 S31: 0.2088 S32: 0.0848 S33: 0.0004 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 71:85) REMARK 3 ORIGIN FOR THE GROUP (A): 13.5039 3.0896 7.8706 REMARK 3 T TENSOR REMARK 3 T11: 0.3103 T22: 0.2761 REMARK 3 T33: 0.2623 T12: 0.0672 REMARK 3 T13: -0.0020 T23: -0.0379 REMARK 3 L TENSOR REMARK 3 L11: 0.4329 L22: 0.4589 REMARK 3 L33: 0.6860 L12: 0.4942 REMARK 3 L13: -0.0997 L23: -0.5162 REMARK 3 S TENSOR REMARK 3 S11: -0.3021 S12: -0.3152 S13: 0.0259 REMARK 3 S21: 0.5119 S22: 0.1884 S23: 0.2411 REMARK 3 S31: -0.4451 S32: -0.5452 S33: 0.0068 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 86:119) REMARK 3 ORIGIN FOR THE GROUP (A): 9.6274 -10.8698 8.4944 REMARK 3 T TENSOR REMARK 3 T11: 0.3680 T22: 0.3142 REMARK 3 T33: 0.3116 T12: 0.0007 REMARK 3 T13: 0.0820 T23: 0.0603 REMARK 3 L TENSOR REMARK 3 L11: 1.2516 L22: 0.6437 REMARK 3 L33: 0.9956 L12: -0.5673 REMARK 3 L13: 0.6968 L23: 0.0952 REMARK 3 S TENSOR REMARK 3 S11: -0.1303 S12: -0.3740 S13: -0.0649 REMARK 3 S21: 0.3211 S22: 0.0689 S23: 0.2727 REMARK 3 S31: 0.1420 S32: -0.4504 S33: -0.0039 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 120:136) REMARK 3 ORIGIN FOR THE GROUP (A): 4.1440 -16.6803 2.5815 REMARK 3 T TENSOR REMARK 3 T11: 0.2590 T22: 0.4706 REMARK 3 T33: 0.4222 T12: -0.1683 REMARK 3 T13: 0.0913 T23: 0.0120 REMARK 3 L TENSOR REMARK 3 L11: 0.3809 L22: 0.5697 REMARK 3 L33: 3.6155 L12: 0.2153 REMARK 3 L13: 0.3056 L23: -0.3975 REMARK 3 S TENSOR REMARK 3 S11: -0.2892 S12: 0.0927 S13: 0.0344 REMARK 3 S21: -0.3095 S22: 0.6147 S23: 1.2492 REMARK 3 S31: 0.1284 S32: -1.4857 S33: -0.1022 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 137:142) REMARK 3 ORIGIN FOR THE GROUP (A): 5.6628 -1.2891 -5.4172 REMARK 3 T TENSOR REMARK 3 T11: 0.3742 T22: 0.5262 REMARK 3 T33: 0.3801 T12: -0.0211 REMARK 3 T13: -0.0882 T23: -0.1749 REMARK 3 L TENSOR REMARK 3 L11: 0.0367 L22: -0.0032 REMARK 3 L33: 0.0037 L12: -0.0056 REMARK 3 L13: 0.0025 L23: -0.0322 REMARK 3 S TENSOR REMARK 3 S11: -0.2098 S12: 1.2492 S13: 0.2510 REMARK 3 S21: -1.4847 S22: 0.1440 S23: 0.1666 REMARK 3 S31: -0.2889 S32: -0.5663 S33: 0.0023 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN A AND RESID 143:196) REMARK 3 ORIGIN FOR THE GROUP (A): 16.0229 -19.2520 -4.7220 REMARK 3 T TENSOR REMARK 3 T11: 0.3960 T22: 0.2113 REMARK 3 T33: 0.3950 T12: -0.1041 REMARK 3 T13: 0.0712 T23: -0.1136 REMARK 3 L TENSOR REMARK 3 L11: 0.7799 L22: 0.3264 REMARK 3 L33: 2.1608 L12: -0.7099 REMARK 3 L13: 0.5179 L23: -0.8875 REMARK 3 S TENSOR REMARK 3 S11: -0.0936 S12: 0.2869 S13: -0.2255 REMARK 3 S21: -0.3916 S22: -0.0068 S23: 0.2218 REMARK 3 S31: 0.4542 S32: -0.2522 S33: -0.0002 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN A AND RESID 197:256) REMARK 3 ORIGIN FOR THE GROUP (A): 25.9889 -13.4809 -0.2807 REMARK 3 T TENSOR REMARK 3 T11: 0.2422 T22: 0.2293 REMARK 3 T33: 0.3086 T12: 0.0340 REMARK 3 T13: 0.0612 T23: -0.0414 REMARK 3 L TENSOR REMARK 3 L11: 0.1516 L22: 2.1094 REMARK 3 L33: 1.1610 L12: 0.3560 REMARK 3 L13: -0.8253 L23: 1.0669 REMARK 3 S TENSOR REMARK 3 S11: -0.1149 S12: 0.0775 S13: -0.0153 REMARK 3 S21: -0.3330 S22: 0.1627 S23: -0.1875 REMARK 3 S31: 0.2748 S32: -0.0580 S33: 0.0032 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN U AND RESID 31:35) REMARK 3 ORIGIN FOR THE GROUP (A): 17.6539 -25.4325 22.8047 REMARK 3 T TENSOR REMARK 3 T11: 1.4912 T22: 0.5319 REMARK 3 T33: 0.6425 T12: -0.0547 REMARK 3 T13: 0.0873 T23: 0.2207 REMARK 3 L TENSOR REMARK 3 L11: 0.1135 L22: 0.0494 REMARK 3 L33: 0.0649 L12: 0.0243 REMARK 3 L13: 0.1388 L23: 0.0222 REMARK 3 S TENSOR REMARK 3 S11: 1.8024 S12: 0.6843 S13: -1.1955 REMARK 3 S21: 1.2911 S22: -0.2723 S23: -0.6675 REMARK 3 S31: 1.0688 S32: -0.0592 S33: 0.0059 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN U AND RESID 36:41) REMARK 3 ORIGIN FOR THE GROUP (A): 25.8176 -35.5043 6.3513 REMARK 3 T TENSOR REMARK 3 T11: 0.7352 T22: 0.2593 REMARK 3 T33: 0.7287 T12: 0.1770 REMARK 3 T13: 0.1308 T23: 0.0441 REMARK 3 L TENSOR REMARK 3 L11: 0.6401 L22: 0.2533 REMARK 3 L33: 0.3384 L12: 0.4042 REMARK 3 L13: 0.5021 L23: 0.1844 REMARK 3 S TENSOR REMARK 3 S11: 0.4425 S12: -0.0930 S13: -0.5033 REMARK 3 S21: 0.3537 S22: -0.4802 S23: -0.0556 REMARK 3 S31: 0.2656 S32: 0.2884 S33: 0.0005 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: (CHAIN V AND RESID 42:46) REMARK 3 ORIGIN FOR THE GROUP (A): 21.2563 -41.8524 6.9056 REMARK 3 T TENSOR REMARK 3 T11: 0.7445 T22: 0.9707 REMARK 3 T33: 0.9244 T12: 0.0125 REMARK 3 T13: 0.2348 T23: -0.1779 REMARK 3 L TENSOR REMARK 3 L11: 0.1004 L22: 0.0722 REMARK 3 L33: 0.0824 L12: -0.0546 REMARK 3 L13: -0.0788 L23: 0.0521 REMARK 3 S TENSOR REMARK 3 S11: 0.9547 S12: 0.1809 S13: -0.7851 REMARK 3 S21: 0.8490 S22: 1.1562 S23: 0.3229 REMARK 3 S31: 0.6187 S32: -0.6012 S33: 0.0058 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: (CHAIN V AND RESID 47:52) REMARK 3 ORIGIN FOR THE GROUP (A): 24.6511 -23.0540 20.3632 REMARK 3 T TENSOR REMARK 3 T11: 0.8767 T22: 0.5883 REMARK 3 T33: 0.5987 T12: 0.3270 REMARK 3 T13: -0.0228 T23: -0.0908 REMARK 3 L TENSOR REMARK 3 L11: 0.4450 L22: 1.4380 REMARK 3 L33: 0.2838 L12: 0.6500 REMARK 3 L13: -0.0478 L23: 0.3500 REMARK 3 S TENSOR REMARK 3 S11: 0.0811 S12: 0.5384 S13: -1.0085 REMARK 3 S21: 2.0654 S22: 0.1784 S23: -1.1955 REMARK 3 S31: -0.1988 S32: -0.9676 S33: 0.0112 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 4B5J 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_1290053626. 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) : 0.9763 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 : 18365 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 38.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.900 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.06000 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 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 61.13500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 34.94000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 34.94000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 91.70250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 34.94000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 34.94000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 30.56750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 34.94000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.94000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 91.70250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 34.94000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.94000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 30.56750 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 61.13500 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: 3490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.2 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH U2003 LIES ON A SPECIAL POSITION. 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: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DG V 51 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC V 52 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 DC V 52 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES 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 SER A 67 -142.70 46.24 REMARK 500 PHE A 171 22.22 -141.32 REMARK 500 REMARK 500 REMARK: NULL 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: 4B5I RELATED DB: PDB REMARK 900 PRODUCT COMPLEX OF NEISSERIA AP ENDONUCLEASE IN PRESENCE OF METAL REMARK 900 IONS 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 4B5J A 1 259 UNP C9X331 C9X331_NEIM8 1 259 DBREF 4B5J U 31 41 PDB 4B5J 4B5J 31 41 DBREF 4B5J V 42 52 PDB 4B5J 4B5J 42 52 SEQADV 4B5J 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 11 DG DC DT DA DC 3DR DC DA DT DC DG SEQRES 1 V 11 DC DG DA DT DG DA DG DT DA DG DC HET 3DR U 36 11 HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETSYN 3DR ABASIC DIDEOXYRIBOSE FORMUL 2 3DR C5 H11 O6 P FORMUL 4 HOH *78(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 GLN A 40 LEU A 44 5 5 HELIX 4 4 SER A 45 LYS A 49 5 5 HELIX 5 5 ASN A 50 MET A 54 5 5 HELIX 6 6 ILE A 86 ARG A 91 1 6 HELIX 7 7 ALA A 116 GLU A 140 1 25 HELIX 8 8 GLN A 155 ASP A 158 5 4 HELIX 9 9 LEU A 172 LYS A 185 1 14 HELIX 10 10 MET A 191 TYR A 196 1 6 HELIX 11 11 GLN A 210 ASP A 215 1 6 HELIX 12 12 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 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 CRYST1 69.880 69.880 122.270 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 0.014310 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014310 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008179 0.00000