PDB Short entry for 2G7F HEADER HYDROLASE 28-FEB-06 2G7F TITLE THE 1.95 A CRYSTAL STRUCTURE OF VIBRIO CHOLERAE EXTRACELLULAR TITLE 2 ENDONUCLEASE I COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDONUCLEASE I; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.21.1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO CHOLERAE; SOURCE 3 ORGANISM_TAXID: 666; SOURCE 4 STRAIN: ATCC14035; SOURCE 5 GENE: ENDA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: TOP10; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PBAD/GIII KEYWDS VIBRIO CHOLERAE NUCLEASE; ENDA; ENDONUCLEASE I; BURIED CHLORIDE, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR B.ALTERMARK,A.O.SMALAAS,N.P.WILLASSEN,R.HELLAND REVDAT 4 30-AUG-23 2G7F 1 REMARK LINK REVDAT 3 24-FEB-09 2G7F 1 VERSN REVDAT 2 26-DEC-06 2G7F 1 TITLE REVDAT 1 31-OCT-06 2G7F 0 JRNL AUTH B.ALTERMARK,A.O.SMALAS,N.P.WILLASSEN,R.HELLAND JRNL TITL THE STRUCTURE OF VIBRIO CHOLERAE EXTRACELLULAR ENDONUCLEASE JRNL TITL 2 I REVEALS THE PRESENCE OF A BURIED CHLORIDE ION. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 62 1387 2006 JRNL REFN ISSN 0907-4449 JRNL PMID 17057343 JRNL DOI 10.1107/S0907444906034196 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.65 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.2 REMARK 3 NUMBER OF REFLECTIONS : 13324 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) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 658 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 REFLECTION IN BIN (WORKING SET) : 433 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE SET COUNT : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1702 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 177 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.03 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.06000 REMARK 3 B22 (A**2) : -0.07000 REMARK 3 B33 (A**2) : 0.12000 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): 0.214 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.183 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.115 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.964 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.902 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1701 ; 0.017 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2309 ; 1.446 ; 1.903 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 207 ; 6.200 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 96 ;37.428 ;24.167 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 263 ;14.002 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;15.244 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 226 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1374 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 764 ; 0.198 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1156 ; 0.293 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 153 ; 0.136 ; 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): 41 ; 0.208 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.157 ; 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): 1063 ; 0.793 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1650 ; 1.335 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 752 ; 2.185 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 659 ; 3.459 ; 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 REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2G7F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-MAR-06. REMARK 100 THE DEPOSITION ID IS D_1000036782. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUL-05 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 6.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13324 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 35.646 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.8 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : 0.07500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 49.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.37800 REMARK 200 R SYM FOR SHELL (I) : 0.37800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 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: 1OUO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 8000 W/V, 0.2 M NA ACETATE, REMARK 280 0.1 M CACODYLATE BUFFER, PH 6.9, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 20.20000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.89000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.37500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.89000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.20000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.37500 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 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 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 20 REMARK 465 PRO A 21 REMARK 465 ILE A 22 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 33 CE NZ REMARK 480 ARG A 36 CG CD NE CZ NH1 NH2 REMARK 480 GLU A 60 CD OE1 OE2 REMARK 480 LYS A 68 CG CD CE NZ REMARK 480 GLN A 90 CD OE1 NE2 REMARK 480 LYS A 100 CD CE NZ REMARK 480 ARG A 104 CB CG CD NE CZ NH1 NH2 REMARK 480 GLN A 148 CG CD OE1 NE2 REMARK 480 LYS A 156 CG CD CE NZ REMARK 480 LYS A 187 CG CD CE NZ REMARK 480 GLN A 191 CG CD OE1 NE2 REMARK 480 LYS A 212 CE NZ REMARK 480 LYS A 215 CE NZ 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 NZ LYS A 68 OE1 GLN A 111 3655 2.14 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 CYS A 46 CB CYS A 46 SG 0.124 REMARK 500 GLN A 90 CG GLN A 90 CD -0.224 REMARK 500 ARG A 104 CD ARG A 104 NE 0.210 REMARK 500 LYS A 187 CE LYS A 187 NZ 0.575 REMARK 500 LYS A 212 CD LYS A 212 CE 0.209 REMARK 500 LYS A 215 CD LYS A 215 CE 0.391 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 36 CA - CB - CG ANGL. DEV. = -30.6 DEGREES REMARK 500 ARG A 36 CB - CG - CD ANGL. DEV. = -18.6 DEGREES REMARK 500 ARG A 104 CD - NE - CZ ANGL. DEV. = -9.0 DEGREES REMARK 500 LYS A 156 CA - CB - CG ANGL. DEV. = 13.7 DEGREES REMARK 500 LYS A 215 CG - CD - CE ANGL. DEV. = 18.9 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 LYS A 68 -47.79 -163.46 REMARK 500 SER A 131 -131.01 58.82 REMARK 500 ASP A 142 59.50 -146.74 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 A 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 79 OE1 REMARK 620 2 ASN A 127 OD1 83.3 REMARK 620 3 HOH A1000 O 101.4 85.1 REMARK 620 4 HOH A1023 O 172.7 99.0 85.7 REMARK 620 5 HOH A1026 O 91.7 86.2 163.2 81.5 REMARK 620 6 HOH A1176 O 84.9 168.2 97.3 92.7 94.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2G7E RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VIBRIO ENDONUCLEASE I AT NEUTRAL PH THE REMARK 900 RESIDUE NUMBERING FOLLOWS THAT OF VIBRIO VULNIFICUS ENDONUCLEASE REMARK 900 (PDB 1OUO) DBREF 2G7F A 20 230 UNP Q2XSK9 Q2XSK9_VIBCH 21 231 SEQRES 1 A 211 ALA PRO ILE SER PHE SER HIS ALA LYS ASN GLU ALA VAL SEQRES 2 A 211 LYS ILE TYR ARG ASP HIS PRO VAL SER PHE TYR CYS GLY SEQRES 3 A 211 CYS GLU ILE ARG TRP GLN GLY LYS LYS GLY ILE PRO ASP SEQRES 4 A 211 LEU GLU SER CYS GLY TYR GLN VAL ARG LYS ASN GLU ASN SEQRES 5 A 211 ARG ALA SER ARG ILE GLU TRP GLU HIS VAL VAL PRO ALA SEQRES 6 A 211 TRP GLN PHE GLY HIS GLN LEU GLN CYS TRP GLN GLN GLY SEQRES 7 A 211 GLY ARG LYS ASN CYS THR ARG THR SER PRO GLU PHE ASN SEQRES 8 A 211 GLN MET GLU ALA ASP LEU HIS ASN LEU THR PRO ALA ILE SEQRES 9 A 211 GLY GLU VAL ASN GLY ASN ARG SER ASN PHE SER PHE SER SEQRES 10 A 211 GLN TRP ASN GLY ILE ASP GLY VAL THR TYR GLY GLN CYS SEQRES 11 A 211 GLU MET GLN VAL ASN PHE LYS GLU ARG THR ALA MET PRO SEQRES 12 A 211 PRO GLU ARG ALA ARG GLY ALA ILE ALA ARG THR TYR LEU SEQRES 13 A 211 TYR MET SER GLU GLN TYR GLY LEU ARG LEU SER LYS ALA SEQRES 14 A 211 GLN ASN GLN LEU MET GLN ALA TRP ASN ASN GLN TYR PRO SEQRES 15 A 211 VAL SER GLU TRP GLU CYS VAL ARG ASP GLN LYS ILE GLU SEQRES 16 A 211 LYS VAL GLN GLY ASN SER ASN ARG PHE VAL ARG GLU GLN SEQRES 17 A 211 CYS PRO ASN HET CL A 300 1 HET MG A 301 1 HETNAM CL CHLORIDE ION HETNAM MG MAGNESIUM ION FORMUL 2 CL CL 1- FORMUL 3 MG MG 2+ FORMUL 4 HOH *177(H2 O) HELIX 1 1 SER A 23 TYR A 35 1 13 HELIX 2 2 ARG A 36 HIS A 38 5 3 HELIX 3 3 LEU A 59 GLY A 63 5 5 HELIX 4 4 ASN A 69 SER A 74 1 6 HELIX 5 5 PRO A 83 HIS A 89 1 7 HELIX 6 6 LEU A 91 SER A 106 1 16 HELIX 7 7 SER A 106 ASP A 115 1 10 HELIX 8 8 GLY A 124 SER A 131 1 8 HELIX 9 9 PRO A 163 GLY A 182 1 20 HELIX 10 10 SER A 186 TYR A 200 1 15 HELIX 11 11 SER A 203 GLY A 218 1 16 HELIX 12 12 ASN A 221 GLU A 226 1 6 SHEET 1 A 2 ILE A 48 GLN A 51 0 SHEET 2 A 2 LYS A 54 PRO A 57 -1 O LYS A 54 N GLN A 51 SHEET 1 B 2 ILE A 76 HIS A 80 0 SHEET 2 B 2 LEU A 119 ILE A 123 -1 O THR A 120 N GLU A 79 SHEET 1 C 4 SER A 134 PHE A 135 0 SHEET 2 C 4 THR A 159 MET A 161 1 O ALA A 160 N SER A 134 SHEET 3 C 4 CYS A 149 ASN A 154 -1 N ASN A 154 O THR A 159 SHEET 4 C 4 VAL A 144 TYR A 146 -1 N VAL A 144 O VAL A 153 SSBOND 1 CYS A 44 CYS A 149 1555 1555 2.06 SSBOND 2 CYS A 46 CYS A 62 1555 1555 1.93 SSBOND 3 CYS A 93 CYS A 102 1555 1555 2.06 SSBOND 4 CYS A 207 CYS A 228 1555 1555 2.02 LINK OE1 GLU A 79 MG MG A 301 1555 1555 2.00 LINK OD1 ASN A 127 MG MG A 301 1555 1555 2.09 LINK MG MG A 301 O HOH A1000 1555 1555 2.07 LINK MG MG A 301 O HOH A1023 1555 1555 2.11 LINK MG MG A 301 O HOH A1026 1555 1555 2.32 LINK MG MG A 301 O HOH A1176 1555 1555 2.09 SITE 1 AC1 4 SER A 41 TYR A 43 CYS A 44 ILE A 123 SITE 1 AC2 6 GLU A 79 ASN A 127 HOH A1000 HOH A1023 SITE 2 AC2 6 HOH A1026 HOH A1176 CRYST1 40.400 64.750 75.780 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 0.024750 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015440 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013200 0.00000