HEADER HYDROLASE 19-DEC-06 2JC4 TITLE 3'-5' EXONUCLEASE (NEXO) FROM NEISSERIA MENINGITIDIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: EXODEOXYRIBONUCLEASE III; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NEISSERIA MENINGITIDIS 3'-5' EXONUCLEASE-NEXO; COMPND 5 EC: 3.1.11.2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEISSERIA MENINGITIDIS; SOURCE 3 ORGANISM_TAXID: 487; SOURCE 4 STRAIN: MC58 SEROGROUP B; SOURCE 5 ATCC: 23251; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ER2566; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PPROEX HTB KEYWDS HYDROLASE, NEISSERIA MENINGITIDIS, REPAIR PHOSPHODIESTERASE, DNA KEYWDS 2 REPAIR, EXONUCLEASE, ENDONUCLEASE EXPDTA X-RAY DIFFRACTION AUTHOR E.P.CARPENTER,A.CORBETT,H.THOMSON,J.ADACHA,K.JENSEN,J.BERGERON, AUTHOR 2 I.KASAMPALIDIS,R.EXLEY,M.WINTERBOTHAM,C.TANG,G.BALDWIN,P.FREEMONT REVDAT 4 16-OCT-24 2JC4 1 REMARK REVDAT 3 13-DEC-23 2JC4 1 LINK REVDAT 2 24-FEB-09 2JC4 1 VERSN REVDAT 1 06-MAR-07 2JC4 0 JRNL AUTH E.P.CARPENTER,A.CORBETT,H.THOMSON,J.ADACHA,K.JENSEN, JRNL AUTH 2 J.BERGERON,I.KASAMPALIDIS,R.EXLEY,M.WINTERBOTHAM,C.TANG, JRNL AUTH 3 G.S.BALDWIN,P.FREEMONT JRNL TITL AP ENDONUCLEASE PARALOGUES WITH DISTINCT ACTIVITIES IN DNA JRNL TITL 2 REPAIR AND BACTERIAL PATHOGENESIS. JRNL REF EMBO J. V. 26 1363 2007 JRNL REFN ISSN 0261-4189 JRNL PMID 17318183 JRNL DOI 10.1038/SJ.EMBOJ.7601593 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 19112 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RAMDOM REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.152 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.180 REMARK 3 FREE R VALUE TEST SET COUNT : 982 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 7.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 19.96 REMARK 3 REFLECTION IN BIN (WORKING SET) : 282 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1950 REMARK 3 BIN FREE R VALUE SET COUNT : 13 REMARK 3 BIN FREE R VALUE : 0.2060 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2028 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 287 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.19300 REMARK 3 B22 (A**2) : 0.07900 REMARK 3 B33 (A**2) : -0.27200 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.155 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.142 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.088 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.953 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2160 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2947 ; 1.501 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 269 ; 6.176 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 103 ;32.938 ;24.175 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 344 ;12.594 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;17.177 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 321 ; 0.107 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1669 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1043 ; 0.203 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1453 ; 0.308 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 225 ; 0.131 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 37 ; 0.213 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 23 ; 0.151 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1318 ; 0.783 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2133 ; 1.372 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 882 ; 2.328 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 811 ; 3.500 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS.FIVE RESIDUES HAVE UNUSUAL PHI PSI VALUES. THESE ARE REMARK 3 RESIDUES SER 10, THR 61, ASN 63, GLU 110 AND HIS 167. THESE REMARK 3 RESIDUES FIT THE ELECTRON DENSITY WELL IN OMIT MAPS AND THEY ARE REMARK 3 THOUGHT TO BE THE RESULT OF USUAL BACKBONE CONFORMATIONS. REMARK 3 RESIDUES CYS 156 AND CYS 168 FORM A PARTIAL DISULPHIDE BRIDGE. REMARK 4 REMARK 4 2JC4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-DEC-06. REMARK 100 THE DEPOSITION ID IS D_1290030723. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.488 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19164 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 24.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.32000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1BIX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN CONCENTRATION 8.7MG/ML BUFFER: REMARK 280 10 MM TRIS, PH 7.0, 100 MM NACL . WELL SOLUTION: 100 MM NA REMARK 280 CACODYLATE PH 6 200 MM NA ACETATE, 15 % PEG 8000. THE REMARK 280 CRYSTALLISATION PLATES USED WERE CORNING ROUND BOTTOM 96 WELL REMARK 280 PLATES. THE CRYSTALLISATION DROPS CONSISTED OF 1UL PROTEIN AND REMARK 280 1UL WELL SOLUTION., PH 6.50 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 23.09650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.31750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.30900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.31750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.09650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.30900 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 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 24 CG OD1 OD2 REMARK 470 LYS A 60 CE NZ REMARK 470 LYS A 161 CD CE NZ REMARK 470 LYS A 230 NZ REMARK 470 GLU A 242 CG CD OE1 OE2 REMARK 470 ARG A 243 CG CD NE CZ NH1 NH2 REMARK 470 TRP A 256 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 256 CZ3 CH2 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 OD1 ASP A 75 O HOH A 2095 2.16 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 10 112.46 94.57 REMARK 500 THR A 61 -44.43 73.18 REMARK 500 ASN A 63 -142.74 61.50 REMARK 500 GLU A 110 -63.11 75.31 REMARK 500 HIS A 167 -32.63 79.89 REMARK 500 HIS A 167 -31.92 79.89 REMARK 500 ASP A 186 97.70 -66.78 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 MG A1256 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 9 OD1 REMARK 620 2 GLU A 34 OE1 88.9 REMARK 620 3 HOH A2029 O 174.1 87.2 REMARK 620 4 HOH A2030 O 93.3 91.1 91.2 REMARK 620 5 HOH A2272 O 93.1 80.1 81.9 169.0 REMARK 620 6 HOH A2273 O 91.9 173.3 91.4 95.6 93.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A1258 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL A 234 O REMARK 620 2 HOH A2110 O 116.3 REMARK 620 3 HOH A2203 O 117.0 125.9 REMARK 620 4 HOH A2254 O 89.4 88.8 100.0 REMARK 620 5 HOH A2255 O 81.0 89.5 90.5 168.3 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 MG A1256 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A1258 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A1260 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1PE A1259 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2HP A1261 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2JC5 RELATED DB: PDB REMARK 900 APURINIC APYRIMIDINIC (AP) ENDONUCLEASE (NAPE) FROM NEISSERIA REMARK 900 MENINGITIDIS DBREF 2JC4 A 1 256 UNP Q9K100 Q9K100_NEIMB 1 256 SEQRES 1 A 256 MET LYS ILE THR THR TRP ASN VAL ASN SER LEU ASN VAL SEQRES 2 A 256 ARG LEU PRO GLN VAL GLN ASN LEU LEU ALA ASP ASN PRO SEQRES 3 A 256 PRO ASP ILE LEU VAL LEU GLN GLU LEU LYS LEU ASP GLN SEQRES 4 A 256 ASP LYS PHE PRO ALA ALA ALA LEU GLN MET MET GLY TRP SEQRES 5 A 256 HIS CYS VAL TRP SER GLY GLN LYS THR TYR ASN GLY VAL SEQRES 6 A 256 ALA ILE VAL SER ARG SER VAL PRO GLN ASP VAL HIS PHE SEQRES 7 A 256 GLY LEU PRO ALA LEU PRO ASP ASP PRO GLN ARG ARG VAL SEQRES 8 A 256 ILE ALA ALA THR VAL SER GLY VAL ARG VAL ILE ASN VAL SEQRES 9 A 256 TYR CYS VAL ASN GLY GLU ALA LEU ASP SER PRO LYS PHE SEQRES 10 A 256 LYS TYR LYS GLU GLN TRP PHE ALA ALA LEU THR GLU PHE SEQRES 11 A 256 VAL ARG ASP GLU MET THR ARG HIS GLY LYS LEU VAL LEU SEQRES 12 A 256 LEU GLY ASP PHE ASN ILE ALA PRO ALA ASP ALA ASP CYS SEQRES 13 A 256 TYR ASP PRO GLU LYS TRP HIS GLU LYS ILE HIS CYS SER SEQRES 14 A 256 SER VAL GLU ARG GLN TRP PHE GLN ASN LEU LEU ASP LEU SEQRES 15 A 256 GLY LEU THR ASP SER LEU ARG GLN VAL HIS PRO GLU GLY SEQRES 16 A 256 ALA PHE TYR THR TRP PHE ASP TYR ARG GLY ALA MET PHE SEQRES 17 A 256 GLN ARG LYS LEU GLY LEU ARG ILE ASP HIS ILE LEU VAL SEQRES 18 A 256 SER PRO ALA MET ALA ALA ALA LEU LYS ASP VAL ARG VAL SEQRES 19 A 256 ASP LEU GLU THR ARG ALA LEU GLU ARG PRO SER ASP HIS SEQRES 20 A 256 ALA PRO VAL THR ALA GLU PHE ASP TRP HET MG A1256 1 HET NA A1257 1 HET NA A1258 1 HET 1PE A1259 16 HET ACT A1260 4 HET 2HP A1261 5 HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM 1PE PENTAETHYLENE GLYCOL HETNAM ACT ACETATE ION HETNAM 2HP DIHYDROGENPHOSPHATE ION HETSYN 1PE PEG400 FORMUL 2 MG MG 2+ FORMUL 3 NA 2(NA 1+) FORMUL 5 1PE C10 H22 O6 FORMUL 6 ACT C2 H3 O2 1- FORMUL 7 2HP H2 O4 P 1- FORMUL 8 HOH *287(H2 O) HELIX 1 1 SER A 10 ASP A 24 1 15 HELIX 2 2 ASP A 38 PHE A 42 5 5 HELIX 3 3 PRO A 43 MET A 49 1 7 HELIX 4 4 SER A 114 THR A 136 1 23 HELIX 5 5 ALA A 152 ASP A 155 5 4 HELIX 6 6 ASP A 158 HIS A 163 5 6 HELIX 7 7 SER A 169 ASP A 181 1 13 HELIX 8 8 SER A 187 HIS A 192 1 6 HELIX 9 9 ALA A 206 LYS A 211 1 6 HELIX 10 10 SER A 222 ALA A 227 1 6 HELIX 11 11 ASP A 235 ALA A 240 1 6 SHEET 1 AA 6 HIS A 53 SER A 57 0 SHEET 2 AA 6 VAL A 65 SER A 69 -1 O VAL A 65 N SER A 57 SHEET 3 AA 6 ILE A 29 GLN A 33 -1 O LEU A 30 N VAL A 68 SHEET 4 AA 6 LYS A 2 ASN A 7 1 O THR A 4 N VAL A 31 SHEET 5 AA 6 VAL A 250 PHE A 254 -1 O VAL A 250 N THR A 5 SHEET 6 AA 6 LEU A 229 VAL A 234 -1 N LYS A 230 O GLU A 253 SHEET 1 AB 6 GLN A 74 PHE A 78 0 SHEET 2 AB 6 VAL A 91 VAL A 96 -1 O ALA A 93 N HIS A 77 SHEET 3 AB 6 VAL A 99 TYR A 105 -1 O VAL A 99 N VAL A 96 SHEET 4 AB 6 LEU A 141 ASP A 146 1 O VAL A 142 N ILE A 102 SHEET 5 AB 6 ASP A 217 VAL A 221 -1 O HIS A 218 N GLY A 145 SHEET 6 AB 6 THR A 185 ASP A 186 -1 O THR A 185 N VAL A 221 SSBOND 1 CYS A 156 CYS A 168 1555 1555 2.03 LINK OD1 ASN A 9 MG MG A1256 1555 1555 2.52 LINK OE1 GLU A 34 MG MG A1256 1555 1555 2.35 LINK O VAL A 234 NA NA A1258 1555 1555 2.28 LINK MG MG A1256 O HOH A2029 1555 1555 2.19 LINK MG MG A1256 O HOH A2030 1555 1555 2.20 LINK MG MG A1256 O HOH A2272 1555 1555 2.23 LINK MG MG A1256 O HOH A2273 1555 1555 2.21 LINK NA NA A1258 O HOH A2110 1555 1555 2.37 LINK NA NA A1258 O HOH A2203 1555 3655 2.35 LINK NA NA A1258 O HOH A2254 1555 1555 2.51 LINK NA NA A1258 O HOH A2255 1555 1555 2.48 SITE 1 AC1 6 ASN A 9 GLU A 34 HOH A2029 HOH A2030 SITE 2 AC1 6 HOH A2272 HOH A2273 SITE 1 AC2 5 VAL A 234 HOH A2110 HOH A2203 HOH A2254 SITE 2 AC2 5 HOH A2255 SITE 1 AC3 5 ASN A 108 HIS A 167 TRP A 200 ILE A 216 SITE 2 AC3 5 HOH A2275 SITE 1 AC4 12 ASP A 113 MET A 135 THR A 136 GLY A 139 SITE 2 AC4 12 PHE A 208 GLN A 209 LYS A 211 LEU A 236 SITE 3 AC4 12 HOH A2138 HOH A2281 HOH A2282 HOH A2283 SITE 1 AC5 5 LYS A 116 HOH A2284 HOH A2285 HOH A2286 SITE 2 AC5 5 HOH A2287 CRYST1 46.193 58.618 88.635 90.00 90.00 90.00 P 21 21 21 4 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 0.021648 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017060 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011282 0.00000