HEADER HYDROLASE/DNA 06-AUG-12 4B5M TITLE NEISSERIA AP ENDONUCLEASE BOUND TO THE SUBSTRATE WITH A CYTOSINE TITLE 2 ORPHAN BASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE EXODEOXYRIBONUCLEASE; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: NEISSERIA AP ENDONUCLEASE; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*3DRP*CP*AP*TP*CP*GP)-3'; COMPND 8 CHAIN: L, M, N; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: 5'-D(*GP*CP*TP*AP*CP)-3'; COMPND 12 CHAIN: U, W, Y; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 4; COMPND 15 MOLECULE: 5'-D(*CP*GP*AP*TP*GP*CP*GP*TP*AP*GP*CP)-3'; COMPND 16 CHAIN: V, X, Z; 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; 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 4B5M 1 LINK REVDAT 3 28-FEB-18 4B5M 1 JRNL REVDAT 2 31-OCT-12 4B5M 1 JRNL REVDAT 1 17-OCT-12 4B5M 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. 2.76 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) : 2.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 30270 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.230 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1529 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 50.1100 - 5.9390 0.97 3128 167 0.1937 0.2457 REMARK 3 2 5.9390 - 4.7151 1.00 3035 149 0.1819 0.2221 REMARK 3 3 4.7151 - 4.1194 0.99 2918 170 0.1676 0.2229 REMARK 3 4 4.1194 - 3.7429 0.96 2804 162 0.2379 0.2756 REMARK 3 5 3.7429 - 3.4747 0.90 2635 125 0.2987 0.3143 REMARK 3 6 3.4747 - 3.2699 0.98 2851 159 0.2769 0.3348 REMARK 3 7 3.2699 - 3.1061 0.99 2847 132 0.2756 0.2999 REMARK 3 8 3.1061 - 2.9709 0.99 2835 151 0.3000 0.3937 REMARK 3 9 2.9709 - 2.8566 0.99 2850 146 0.3424 0.3755 REMARK 3 10 2.8566 - 2.7580 0.99 2838 168 0.3939 0.4965 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.95 REMARK 3 K_SOL : 0.30 REMARK 3 B_SOL : 50.46 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.410 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.060 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 68.73 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 14.08870 REMARK 3 B22 (A**2) : 14.08870 REMARK 3 B33 (A**2) : -28.17730 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 : 0.009 8119 REMARK 3 ANGLE : 1.005 10917 REMARK 3 CHIRALITY : 0.066 1120 REMARK 3 PLANARITY : 0.003 1188 REMARK 3 DIHEDRAL : 21.383 2974 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN A AND (RESSEQ 1:257 ) REMARK 3 SELECTION : CHAIN B AND (RESSEQ 1:257 ) REMARK 3 ATOM PAIRS NUMBER : 2077 REMARK 3 RMSD : 0.023 REMARK 3 NCS OPERATOR : 2 REMARK 3 REFERENCE SELECTION: CHAIN A AND (RESSEQ 1:257 ) REMARK 3 SELECTION : CHAIN C AND (RESSEQ 1:257 ) REMARK 3 ATOM PAIRS NUMBER : 2077 REMARK 3 RMSD : 0.024 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4B5M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1290053636. 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) : 1.0 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 : 30548 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.760 REMARK 200 RESOLUTION RANGE LOW (A) : 50.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 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 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 (%): 52.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 191.29000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 38.52500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 38.52500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 95.64500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 38.52500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 38.52500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 286.93500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 38.52500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.52500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 95.64500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 38.52500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.52500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 286.93500 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 191.29000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: 3430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.9 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, L, 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 350 REMARK 350 BIOMOLECULE: 2 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: 3420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, M, W, 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 350 REMARK 350 BIOMOLECULE: 3 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: 3420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.8 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, N, Y, Z 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 258 REMARK 465 GLU A 259 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 GLU B 259 O REMARK 470 GLU C 259 O 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 PRO A 227 C - N - CA ANGL. DEV. = 10.0 DEGREES REMARK 500 PRO B 227 C - N - CA ANGL. DEV. = 9.8 DEGREES REMARK 500 PRO C 227 C - N - CA ANGL. DEV. = 9.7 DEGREES REMARK 500 DC U 35 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT V 45 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG V 51 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC W 32 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT W 33 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DC W 35 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC X 42 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA X 44 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT X 49 O4' - C1' - N1 ANGL. DEV. = -5.3 DEGREES REMARK 500 DC Y 32 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DT Y 33 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC Y 35 O5' - C5' - C4' ANGL. DEV. = -5.2 DEGREES REMARK 500 DC Y 35 O4' - C1' - N1 ANGL. DEV. = 6.6 DEGREES REMARK 500 DT Z 45 N3 - C4 - O4 ANGL. DEV. = 3.9 DEGREES REMARK 500 DG Z 46 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC Z 47 O4' - C4' - C3' ANGL. DEV. = -3.9 DEGREES REMARK 500 DG Z 48 O4' - C1' - N9 ANGL. DEV. = -4.6 DEGREES REMARK 500 DT Z 49 O4' - C1' - N1 ANGL. DEV. = -5.1 DEGREES REMARK 500 DA Z 50 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DG Z 51 O4' - C1' - N9 ANGL. DEV. = 2.1 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 HIS A 52 29.28 49.68 REMARK 500 GLU A 62 33.53 -79.47 REMARK 500 SER A 67 -138.48 42.86 REMARK 500 GLU A 88 -34.84 -37.71 REMARK 500 PHE A 100 76.71 -111.79 REMARK 500 ASN A 161 58.16 -101.40 REMARK 500 PHE A 171 25.10 -144.23 REMARK 500 HIS A 184 -61.81 -96.96 REMARK 500 LYS B 49 -31.60 -130.88 REMARK 500 HIS B 52 29.74 49.60 REMARK 500 GLU B 62 33.59 -79.60 REMARK 500 SER B 67 -138.29 43.41 REMARK 500 GLU B 88 -34.54 -37.64 REMARK 500 PHE B 100 75.73 -113.22 REMARK 500 ASN B 161 58.91 -100.36 REMARK 500 PHE B 171 26.01 -143.37 REMARK 500 HIS B 184 -62.05 -96.76 REMARK 500 LYS C 49 -31.69 -130.83 REMARK 500 HIS C 52 28.25 49.52 REMARK 500 GLU C 62 32.93 -78.80 REMARK 500 SER C 67 -138.15 42.96 REMARK 500 GLU C 88 -34.80 -36.87 REMARK 500 PHE C 100 76.58 -112.18 REMARK 500 ASN C 161 59.94 -101.80 REMARK 500 PHE C 171 26.01 -143.94 REMARK 500 HIS C 184 -63.15 -97.59 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: 4B5J RELATED DB: PDB REMARK 900 NEISSERIA AP ENDONUCLEASE BOUND TO THE SUBSTRATE WITH AN ORPHAN REMARK 900 ADENINE BASE DBREF 4B5M A 1 259 UNP C9X331 C9X331_NEIM8 1 259 DBREF 4B5M B 1 259 UNP C9X331 C9X331_NEIM8 1 259 DBREF 4B5M C 1 259 UNP C9X331 C9X331_NEIM8 1 259 DBREF 4B5M L 36 41 PDB 4B5M 4B5M 36 41 DBREF 4B5M M 36 41 PDB 4B5M 4B5M 36 41 DBREF 4B5M N 36 41 PDB 4B5M 4B5M 36 41 DBREF 4B5M U 31 35 PDB 4B5M 4B5M 31 35 DBREF 4B5M V 42 52 PDB 4B5M 4B5M 42 52 DBREF 4B5M W 31 35 PDB 4B5M 4B5M 31 35 DBREF 4B5M X 42 52 PDB 4B5M 4B5M 42 52 DBREF 4B5M Y 31 35 PDB 4B5M 4B5M 31 35 DBREF 4B5M Z 42 52 PDB 4B5M 4B5M 42 52 SEQADV 4B5M GLY A 101 UNP C9X331 ASP 101 CONFLICT SEQADV 4B5M GLY B 101 UNP C9X331 ASP 101 CONFLICT SEQADV 4B5M GLY C 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 B 259 MET LEU LYS ILE ILE SER ALA ASN VAL ASN GLY ILE ARG SEQRES 2 B 259 SER ALA TYR LYS LYS GLY PHE TYR GLU TYR ILE ALA ALA SEQRES 3 B 259 SER GLY ALA ASP ILE VAL CYS VAL GLN GLU LEU LYS ALA SEQRES 4 B 259 GLN GLU ALA ASP LEU SER ALA ASP MET LYS ASN PRO HIS SEQRES 5 B 259 GLY MET HIS GLY HIS TRP HIS CYS ALA GLU LYS ARG GLY SEQRES 6 B 259 TYR SER GLY VAL ALA VAL TYR SER LYS ARG LYS PRO ASP SEQRES 7 B 259 ASN VAL GLN ILE GLY MET GLY ILE GLU GLU PHE ASP ARG SEQRES 8 B 259 GLU GLY ARG PHE VAL ARG CYS ASP PHE GLY ARG LEU SER SEQRES 9 B 259 VAL ILE SER LEU TYR LEU PRO SER GLY SER SER ALA GLU SEQRES 10 B 259 GLU ARG GLN GLN VAL LYS TYR ARG PHE LEU ASP ALA PHE SEQRES 11 B 259 TYR PRO MET LEU GLU ALA MET LYS ASN GLU GLY ARG ASP SEQRES 12 B 259 ILE VAL VAL CYS GLY ASP TRP ASN ILE ALA HIS GLN ASN SEQRES 13 B 259 ILE ASP LEU LYS ASN TRP LYS GLY ASN GLN LYS ASN SER SEQRES 14 B 259 GLY PHE LEU PRO GLU GLU ARG GLU TRP ILE GLY LYS VAL SEQRES 15 B 259 ILE HIS LYS LEU GLY TRP THR ASP MET TRP ARG THR LEU SEQRES 16 B 259 TYR PRO ASP VAL PRO GLY TYR THR TRP TRP SER ASN ARG SEQRES 17 B 259 GLY GLN ALA TYR ALA LYS ASP VAL GLY TRP ARG ILE ASP SEQRES 18 B 259 TYR GLN MET VAL THR PRO GLU LEU ALA ALA LYS ALA VAL SEQRES 19 B 259 SER ALA HIS VAL TYR LYS ASP GLU LYS PHE SER ASP HIS SEQRES 20 B 259 ALA PRO LEU VAL VAL GLU TYR ASP TYR ALA ALA GLU SEQRES 1 C 259 MET LEU LYS ILE ILE SER ALA ASN VAL ASN GLY ILE ARG SEQRES 2 C 259 SER ALA TYR LYS LYS GLY PHE TYR GLU TYR ILE ALA ALA SEQRES 3 C 259 SER GLY ALA ASP ILE VAL CYS VAL GLN GLU LEU LYS ALA SEQRES 4 C 259 GLN GLU ALA ASP LEU SER ALA ASP MET LYS ASN PRO HIS SEQRES 5 C 259 GLY MET HIS GLY HIS TRP HIS CYS ALA GLU LYS ARG GLY SEQRES 6 C 259 TYR SER GLY VAL ALA VAL TYR SER LYS ARG LYS PRO ASP SEQRES 7 C 259 ASN VAL GLN ILE GLY MET GLY ILE GLU GLU PHE ASP ARG SEQRES 8 C 259 GLU GLY ARG PHE VAL ARG CYS ASP PHE GLY ARG LEU SER SEQRES 9 C 259 VAL ILE SER LEU TYR LEU PRO SER GLY SER SER ALA GLU SEQRES 10 C 259 GLU ARG GLN GLN VAL LYS TYR ARG PHE LEU ASP ALA PHE SEQRES 11 C 259 TYR PRO MET LEU GLU ALA MET LYS ASN GLU GLY ARG ASP SEQRES 12 C 259 ILE VAL VAL CYS GLY ASP TRP ASN ILE ALA HIS GLN ASN SEQRES 13 C 259 ILE ASP LEU LYS ASN TRP LYS GLY ASN GLN LYS ASN SER SEQRES 14 C 259 GLY PHE LEU PRO GLU GLU ARG GLU TRP ILE GLY LYS VAL SEQRES 15 C 259 ILE HIS LYS LEU GLY TRP THR ASP MET TRP ARG THR LEU SEQRES 16 C 259 TYR PRO ASP VAL PRO GLY TYR THR TRP TRP SER ASN ARG SEQRES 17 C 259 GLY GLN ALA TYR ALA LYS ASP VAL GLY TRP ARG ILE ASP SEQRES 18 C 259 TYR GLN MET VAL THR PRO GLU LEU ALA ALA LYS ALA VAL SEQRES 19 C 259 SER ALA HIS VAL TYR LYS ASP GLU LYS PHE SER ASP HIS SEQRES 20 C 259 ALA PRO LEU VAL VAL GLU TYR ASP TYR ALA ALA GLU SEQRES 1 L 6 3DR DC DA DT DC DG SEQRES 1 M 6 3DR DC DA DT DC DG SEQRES 1 N 6 3DR DC DA DT DC DG SEQRES 1 U 5 DG DC DT DA DC SEQRES 1 V 11 DC DG DA DT DG DC DG DT DA DG DC SEQRES 1 W 5 DG DC DT DA DC SEQRES 1 X 11 DC DG DA DT DG DC DG DT DA DG DC SEQRES 1 Y 5 DG DC DT DA DC SEQRES 1 Z 11 DC DG DA DT DG DC DG DT DA DG DC HET 3DR L 36 12 HET 3DR M 36 12 HET 3DR N 36 12 HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETSYN 3DR ABASIC DIDEOXYRIBOSE FORMUL 4 3DR 3(C5 H11 O6 P) 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 HIS A 184 1 13 HELIX 10 10 MET A 191 TYR A 196 1 6 HELIX 11 11 THR A 226 LYS A 232 1 7 HELIX 12 12 GLY B 11 LYS B 18 1 8 HELIX 13 13 GLY B 19 SER B 27 1 9 HELIX 14 14 GLN B 40 LEU B 44 5 5 HELIX 15 15 ASN B 50 MET B 54 5 5 HELIX 16 16 ILE B 86 ARG B 91 1 6 HELIX 17 17 ALA B 116 GLU B 140 1 25 HELIX 18 18 GLN B 155 ASP B 158 5 4 HELIX 19 19 LEU B 172 HIS B 184 1 13 HELIX 20 20 MET B 191 TYR B 196 1 6 HELIX 21 21 THR B 226 LYS B 232 1 7 HELIX 22 22 GLY C 11 LYS C 18 1 8 HELIX 23 23 GLY C 19 SER C 27 1 9 HELIX 24 24 GLN C 40 LEU C 44 5 5 HELIX 25 25 SER C 45 LYS C 49 5 5 HELIX 26 26 ASN C 50 MET C 54 5 5 HELIX 27 27 ILE C 86 ARG C 91 1 6 HELIX 28 28 ALA C 116 GLU C 140 1 25 HELIX 29 29 GLN C 155 ASP C 158 5 4 HELIX 30 30 LEU C 172 HIS C 184 1 13 HELIX 31 31 MET C 191 TYR C 196 1 6 HELIX 32 32 THR C 226 LYS C 232 1 7 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 BA 6 HIS B 55 HIS B 59 0 SHEET 2 BA 6 VAL B 69 SER B 73 -1 O VAL B 69 N HIS B 59 SHEET 3 BA 6 ILE B 31 GLN B 35 -1 O VAL B 32 N TYR B 72 SHEET 4 BA 6 LEU B 2 ASN B 8 1 O ILE B 5 N CYS B 33 SHEET 5 BA 6 LEU B 250 TYR B 254 -1 O LEU B 250 N SER B 6 SHEET 6 BA 6 ALA B 233 VAL B 238 -1 N VAL B 234 O GLU B 253 SHEET 1 BB 6 ASN B 79 ILE B 82 0 SHEET 2 BB 6 PHE B 95 PHE B 100 -1 O ARG B 97 N GLN B 81 SHEET 3 BB 6 LEU B 103 TYR B 109 -1 O LEU B 103 N PHE B 100 SHEET 4 BB 6 ASP B 143 ASP B 149 1 O ASP B 143 N SER B 104 SHEET 5 BB 6 ASP B 221 VAL B 225 -1 O TYR B 222 N GLY B 148 SHEET 6 BB 6 THR B 189 ASP B 190 -1 O THR B 189 N VAL B 225 SHEET 1 CA 6 HIS C 55 HIS C 59 0 SHEET 2 CA 6 VAL C 69 SER C 73 -1 O VAL C 69 N HIS C 59 SHEET 3 CA 6 ILE C 31 GLN C 35 -1 O VAL C 32 N TYR C 72 SHEET 4 CA 6 LEU C 2 ASN C 8 1 O ILE C 5 N CYS C 33 SHEET 5 CA 6 LEU C 250 TYR C 254 -1 O LEU C 250 N SER C 6 SHEET 6 CA 6 ALA C 233 VAL C 238 -1 N VAL C 234 O GLU C 253 SHEET 1 CB 6 ASN C 79 ILE C 82 0 SHEET 2 CB 6 PHE C 95 PHE C 100 -1 O ARG C 97 N GLN C 81 SHEET 3 CB 6 LEU C 103 TYR C 109 -1 O LEU C 103 N PHE C 100 SHEET 4 CB 6 ASP C 143 ASP C 149 1 O ASP C 143 N SER C 104 SHEET 5 CB 6 ASP C 221 VAL C 225 -1 O TYR C 222 N GLY C 148 SHEET 6 CB 6 THR C 189 ASP C 190 -1 O THR C 189 N VAL C 225 LINK O3' 3DR L 36 P DC L 37 1555 1555 1.61 LINK O3' 3DR M 36 P DC M 37 1555 1555 1.61 LINK O3' 3DR N 36 P DC N 37 1555 1555 1.60 CRYST1 77.050 77.050 382.580 90.00 90.00 90.00 P 41 21 2 24 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 0.012979 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012979 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002614 0.00000