HEADER HYDROLASE 19-DEC-06 2JC5 TITLE APURINIC APYRIMIDINIC (AP) ENDONUCLEASE (NAPE) FROM NEISSERIA TITLE 2 MENINGITIDIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: EXODEOXYRIBONUCLEASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: APURINIC APYRIMIDINIC AP ENDONUCLEASE FROM NEISSERIA COMPND 5 MENINGITIDIS - NAPE; COMPND 6 EC: 3.1.11.2; COMPND 7 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: 23151; 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.S.BALDWIN,P.FREEMONT REVDAT 4 13-DEC-23 2JC5 1 LINK REVDAT 3 08-MAY-19 2JC5 1 REMARK REVDAT 2 24-FEB-09 2JC5 1 VERSN REVDAT 1 06-MAR-07 2JC5 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. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.53 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 35412 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.123 REMARK 3 R VALUE (WORKING SET) : 0.120 REMARK 3 FREE R VALUE : 0.159 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1774 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) : 6.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 29.53 REMARK 3 REFLECTION IN BIN (WORKING SET) : 423 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1860 REMARK 3 BIN FREE R VALUE SET COUNT : 25 REMARK 3 BIN FREE R VALUE : 0.1740 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2073 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 313 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.64 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 8.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.33600 REMARK 3 B22 (A**2) : 0.65400 REMARK 3 B33 (A**2) : -0.30500 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.02200 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.085 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.066 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.023 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.298 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.975 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.963 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2237 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3045 ; 1.330 ; 1.937 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 290 ; 6.191 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 105 ;36.826 ;23.905 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 371 ;10.996 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;13.080 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 308 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2549 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 443 ; 0.263 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1062 ; 0.185 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 222 ; 0.161 ; 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): 15 ; 0.722 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 21 ; 0.479 ; 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): 1421 ; 1.986 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2161 ; 2.506 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1029 ; 2.160 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 871 ; 2.868 ; 3.000 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 : BABINET MODEL PLUS MASK 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. THE FOLLOWING RESIDUES HAVE ATOMS MISSING FROM THE REMARK 3 SIDECHAINS BECAUSE THERE WAS NO DENSITY FOR THESE ATOMS IN THE REMARK 3 ELECTRON DENSITY MAPS ARG 64, ARG 75, GLU 87, GLU 177, LYS 181, REMARK 3 LYS 185, AND GLU 259. REMARK 4 REMARK 4 2JC5 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_1290030852. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUL-05 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 9.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 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 : 35560 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.27000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.500 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 (%): 38.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24 WELL LINBRO PLATES USED FOR HANGING REMARK 280 DROP EXPERIMENTS WITH 0.5 UL PROTEIN AND 0.5 UL WELL SOLUTION REMARK 280 FOR THE DROPS. PROTEIN CONCENTRATION 20 MG/ML, IN 10 MM TRIS, PH REMARK 280 7.0 AND 100 MM NACL. THE WELL SOLUTION CONTAINED 20% PEG 20000, REMARK 280 0.1 M BICINE PH 9.0, 2% DIOXANE., PH 9.00, VAPOR DIFFUSION, REMARK 280 HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 39.75550 REMARK 290 SMTRY3 2 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 ARG A 64 CZ NH1 NH2 REMARK 470 ARG A 75 NE CZ NH1 NH2 REMARK 470 GLU A 87 CD OE1 OE2 REMARK 470 LYS A 163 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 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 H1 HOH A 2043 H2 HOH A 2045 0.00 REMARK 500 H1 HOH A 2043 H2 HOH A 2291 0.00 REMARK 500 H1 HOH A 2043 H1 HOH A 2292 0.00 REMARK 500 H2 HOH A 2045 H2 HOH A 2291 0.00 REMARK 500 H2 HOH A 2045 H1 HOH A 2292 0.00 REMARK 500 H2 HOH A 2291 H1 HOH A 2292 0.00 REMARK 500 HZ3 LYS A 17 H1 HOH A 2022 0.88 REMARK 500 HZ1 LYS A 74 H1 HOH A 2109 0.92 REMARK 500 HE2 HIS A 154 H1 HOH A 2181 0.94 REMARK 500 H2 HOH A 2136 H1 HOH A 2299 0.95 REMARK 500 HE22 GLN A 81 H1 HOH A 2124 1.04 REMARK 500 H1 HOH A 2095 H2 HOH A 2233 1.06 REMARK 500 HD22 ASN A 79 H1 HOH A 2118 1.10 REMARK 500 HZ2 LYS A 49 H2 HOH A 2048 1.11 REMARK 500 HZ1 LYS A 3 H2 HOH A 2003 1.13 REMARK 500 HZ3 LYS A 240 H1 HOH A 2281 1.15 REMARK 500 HD22 ASN A 156 H1 HOH A 2190 1.15 REMARK 500 H PHE A 244 H1 HOH A 2294 1.18 REMARK 500 HD22 ASN A 168 H2 HOH A 2214 1.18 REMARK 500 H2 HOH A 2066 H1 HOH A 2076 1.18 REMARK 500 H GLN A 210 H2 HOH A 2256 1.18 REMARK 500 HH22 ARG A 102 H1 HOH A 2174 1.20 REMARK 500 HZ3 LYS A 243 H2 HOH A 2288 1.20 REMARK 500 HZ1 LYS A 160 H1 HOH A 2197 1.20 REMARK 500 H1 HOH A 2276 H2 HOH A 2277 1.20 REMARK 500 HH TYR A 202 H1 HOH A 2192 1.21 REMARK 500 H GLN A 210 H2 HOH A 2256 1.21 REMARK 500 HZ3 LYS A 74 H2 HOH A 2108 1.21 REMARK 500 H GLU A 88 H1 HOH A 2133 1.22 REMARK 500 H2 HOH A 2004 H1 HOH A 2052 1.22 REMARK 500 H ASN A 156 H1 HOH A 2184 1.25 REMARK 500 H1 HOH A 2180 H2 HOH A 2293 1.26 REMARK 500 H SER A 169 H2 HOH A 2216 1.27 REMARK 500 H2 HOH A 2073 H1 HOH A 2074 1.27 REMARK 500 H1 HOH A 2058 H2 HOH A 2158 1.27 REMARK 500 HE1 TRP A 218 H2 HOH A 2263 1.29 REMARK 500 HE2 HIS A 247 H2 HOH A 2293 1.30 REMARK 500 H ALA A 258 H2 HOH A 2306 1.31 REMARK 500 H LYS A 63 H1 HOH A 2137 1.33 REMARK 500 H1 HOH A 2057 H2 HOH A 2154 1.35 REMARK 500 NZ LYS A 3 H2 HOH A 2003 1.56 REMARK 500 HD22 ASN A 79 O HOH A 2118 1.56 REMARK 500 NZ LYS A 240 H1 HOH A 2281 1.56 REMARK 500 HG CYS A 60 O HOH A 2049 1.60 REMARK 500 OE1 GLU A 36 O HOH A 2045 1.77 REMARK 500 OD2 ASP A 47 O HOH A 2061 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 H GLU A 118 H2 HOH A 2170 1455 1.12 REMARK 500 H1 HOH A 2041 H2 HOH A 2196 1554 1.16 REMARK 500 H1 HOH A 2251 H2 HOH A 2273 1455 1.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG A 91 NE ARG A 91 CZ 3.303 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 91 CD - NE - CZ ANGL. DEV. = -82.4 DEGREES REMARK 500 ARG A 91 NE - CZ - NH1 ANGL. DEV. = 36.6 DEGREES REMARK 500 ARG A 91 NE - CZ - NH2 ANGL. DEV. = -37.3 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 GLU A 36 63.41 62.21 REMARK 500 GLU A 36 63.19 64.66 REMARK 500 SER A 67 -147.42 54.73 REMARK 500 ASN A 161 72.09 -108.00 REMARK 500 PHE A 171 28.99 -143.98 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 A1260 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 10 OD1 REMARK 620 2 HOH A2043 O 86.8 REMARK 620 3 HOH A2045 O 176.5 95.1 REMARK 620 4 HOH A2291 O 95.4 87.7 81.8 REMARK 620 5 HOH A2292 O 89.9 176.6 88.3 93.1 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 A1260 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BCN A1261 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DIO A1264 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DIO A1265 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1262 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1263 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2JC4 RELATED DB: PDB REMARK 900 3'-5' EXONUCLEASE (NEXO) FROM NEISSERIA MENINGITIDIS DBREF 2JC5 A 1 259 UNP Q7DD47 Q7DD47_NEIMB 1 259 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 HET MG A1260 1 HET BCN A1261 23 HET GOL A1262 14 HET GOL A1263 14 HET DIO A1264 14 HET DIO A1265 14 HETNAM MG MAGNESIUM ION HETNAM BCN BICINE HETNAM GOL GLYCEROL HETNAM DIO 1,4-DIETHYLENE DIOXIDE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 MG MG 2+ FORMUL 3 BCN C6 H13 N O4 FORMUL 4 GOL 2(C3 H8 O3) FORMUL 6 DIO 2(C4 H8 O2) FORMUL 8 HOH *313(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 ASN A 50 1 6 HELIX 5 5 PRO A 51 MET A 54 5 4 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 GLY A 209 LYS A 214 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 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 OD1 ASN A 10 MG MG A1260 1555 1555 2.31 LINK MG MG A1260 O HOH A2043 1555 1555 1.85 LINK MG MG A1260 O HOH A2045 1555 1555 1.82 LINK MG MG A1260 O HOH A2291 1555 1555 2.03 LINK MG MG A1260 O HOH A2292 1555 1555 1.88 SITE 1 AC1 6 ASN A 10 GLU A 36 HOH A2043 HOH A2045 SITE 2 AC1 6 HOH A2291 HOH A2292 SITE 1 AC2 8 SER A 112 GLY A 113 SER A 114 LYS A 123 SITE 2 AC2 8 ASN A 151 SER A 169 GLU A 228 HOH A2303 SITE 1 AC3 3 TYR A 124 GLU A 174 HOH A2311 SITE 1 AC4 6 TYR A 16 TYR A 21 ASP A 47 HOH A2062 SITE 2 AC4 6 HOH A2312 HOH A2313 SITE 1 AC5 9 ASP A 30 ILE A 31 LYS A 74 ARG A 75 SITE 2 AC5 9 PHE A 100 ALA A 258 HOH A2037 HOH A2306 SITE 3 AC5 9 HOH A2307 SITE 1 AC6 6 TYR A 212 ASP A 215 LYS A 240 HOH A2281 SITE 2 AC6 6 HOH A2309 HOH A2310 CRYST1 38.156 79.511 41.045 90.00 107.22 90.00 P 1 21 1 2 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 0.026208 0.000000 0.008123 0.00000 SCALE2 0.000000 0.012577 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025507 0.00000