PDB Short entry for 4ABT HEADER HYDROLASE/DNA 11-DEC-11 4ABT TITLE CRYSTAL STRUCTURE OF TYPE IIF RESTRICTION ENDONUCLEASE NGOMIV WITH TITLE 2 COGNATE UNCLEAVED DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYPE-2 RESTRICTION ENZYME NGOMIV; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: TYPE IIF RESTRICTION ENDONUCLEASE NGOMIV, R.NGOMIV, COMPND 5 ENDONUCLEASE NGOMIV, TYPE II RESTRICTION ENZYME NGOMIV; COMPND 6 EC: 3.1.21.4; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: 5'-D(*TP*GP*CP*GP*CP*CP*GP*GP*CP*GP*CP)-3'; COMPND 10 CHAIN: E, G; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEISSERIA GONORRHOEAE; SOURCE 3 ORGANISM_TAXID: 485; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: HMS 174 DE3; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET15B; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: NEISSERIA GONORRHOEAE; SOURCE 12 ORGANISM_TAXID: 485 KEYWDS HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR E.N.MANAKOVA,S.GRAZULIS,M.ZAREMBA,G.TAMULAITIENE,D.GOLOVENKO, AUTHOR 2 V.SIKSNYS REVDAT 4 20-DEC-23 4ABT 1 REMARK LINK REVDAT 3 17-JUL-19 4ABT 1 REMARK REVDAT 2 10-AUG-16 4ABT 1 REMARK MASTER REVDAT 1 28-DEC-11 4ABT 0 JRNL AUTH E.N.MANAKOVA,S.GRAZULIS,M.ZAREMBA,G.TAMULAITIENE, JRNL AUTH 2 D.GOLOVENKO,V.SIKSNYS JRNL TITL STRUCTURE OF TYPE IIF RESTRICTION ENDONUCLEASE NGOMIV WITH JRNL TITL 2 COGNATE UNCLEAVED DNA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH E.MANAKOVA,S.GRAZULIS,M.ZAREMBA,G.TAMULAITIENE,D.GOLOVENKO, REMARK 1 AUTH 2 V.SIKSNYS REMARK 1 TITL STRUCTURAL MECHANISMS OF THE DEGENERATE SEQUENCE RECOGNITION REMARK 1 TITL 2 BY BSE634I RESTRICTION ENDONUCLEASE. REMARK 1 REF NUCLEIC ACIDS RES. V. 40 6741 2012 REMARK 1 REFN ISSN 0305-1048 REMARK 1 PMID 22495930 REMARK 1 DOI 10.1093/NAR/GKS300 REMARK 2 REMARK 2 RESOLUTION. 2.22 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0070 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) : 2.22 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 11.95 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 25981 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) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2859 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) : 2.22 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.27 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1562 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.58 REMARK 3 BIN R VALUE (WORKING SET) : 0.2720 REMARK 3 BIN FREE R VALUE SET COUNT : 206 REMARK 3 BIN FREE R VALUE : 0.3370 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4476 REMARK 3 NUCLEIC ACID ATOMS : 444 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 246 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.39000 REMARK 3 B22 (A**2) : -0.62000 REMARK 3 B33 (A**2) : 1.02000 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): 0.373 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.236 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.915 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4836 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6655 ; 1.815 ; 2.076 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 549 ; 6.477 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 204 ;36.023 ;24.216 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 726 ;15.773 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 34 ;16.884 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 775 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3516 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 2752 ; 0.946 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4420 ; 1.744 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2084 ; 2.717 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2233 ; 4.161 ; 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 : 1.40 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. U VALUES REFINED INDIVIDUALLY REMARK 4 REMARK 4 4ABT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-DEC-11. REMARK 100 THE DEPOSITION ID IS D_1290050671. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-NOV-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.812 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28869 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.220 REMARK 200 RESOLUTION RANGE LOW (A) : 11.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.22 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.34000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1FIU REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NAHEPES 0.1M, CACL2 0.2M, MPD 24%, PH REMARK 280 7.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 34.44950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.04050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.44950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.04050 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: OCTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 29170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 40210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -155.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, E, G 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 BIOMT1 2 -1.000000 0.000000 0.000000 68.89900 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 180.16200 REMARK 350 BIOMT3 2 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 CA CA E1000 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2077 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2094 LIES ON A SPECIAL POSITION. REMARK 375 HOH B2076 LIES ON A SPECIAL POSITION. REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 GLY A 98 REMARK 475 SER A 99 REMARK 475 ARG A 100 REMARK 475 ASN A 101 REMARK 475 ARG A 102 REMARK 475 LEU A 103 REMARK 475 SER A 133 REMARK 475 ASP A 134 REMARK 475 TYR A 135 REMARK 475 GLY A 173 REMARK 475 ASN A 174 REMARK 475 GLY A 175 REMARK 475 GLY B 98 REMARK 475 SER B 99 REMARK 475 ARG B 100 REMARK 475 ASN B 101 REMARK 475 ARG B 102 REMARK 475 SER B 133 REMARK 475 ASP B 134 REMARK 475 TYR B 135 REMARK 475 ASN B 174 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 ARG A 27 NE CZ NH1 NH2 REMARK 480 GLN A 78 CG CD OE1 NE2 REMARK 480 LYS A 95 CD CE NZ REMARK 480 ARG A 107 NE CZ NH1 NH2 REMARK 480 GLU A 123 CG CD OE1 OE2 REMARK 480 ASN A 124 CG OD1 ND2 REMARK 480 GLU A 126 CG CD OE1 OE2 REMARK 480 LYS A 272 CE NZ REMARK 480 ARG B 27 CD NE CZ NH1 NH2 REMARK 480 LYS B 45 CD CE NZ REMARK 480 ASP B 49 CG OD1 OD2 REMARK 480 LYS B 83 CE NZ REMARK 480 LYS B 95 CD CE NZ REMARK 480 LEU B 103 CB CG CD1 CD2 REMARK 480 LYS B 119 CG CD CE NZ REMARK 480 GLU B 122 CG CD OE1 OE2 REMARK 480 GLU B 123 CG CD OE1 OE2 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 DC E 11 O3' DC E 11 C3' -0.063 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 B 59 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 DT E 1 N3 - C4 - O4 ANGL. DEV. = 4.9 DEGREES REMARK 500 DT E 1 C5 - C4 - O4 ANGL. DEV. = -5.2 DEGREES REMARK 500 DG E 2 O4' - C1' - N9 ANGL. DEV. = -5.6 DEGREES REMARK 500 DG E 4 C3' - O3' - P ANGL. DEV. = 10.9 DEGREES REMARK 500 DG E 8 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DG E 10 O4' - C1' - N9 ANGL. DEV. = -8.2 DEGREES REMARK 500 DT G 1 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 DT G 1 C3' - O3' - P ANGL. DEV. = 8.7 DEGREES REMARK 500 DG G 2 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 DG G 2 C3' - O3' - P ANGL. DEV. = 9.0 DEGREES REMARK 500 DG G 4 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DC G 5 O4' - C4' - C3' ANGL. DEV. = -2.7 DEGREES REMARK 500 DC G 6 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DC G 6 C3' - O3' - P ANGL. DEV. = 9.4 DEGREES REMARK 500 DG G 10 O4' - C1' - N9 ANGL. DEV. = -6.3 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 SER A 133 134.25 -37.36 REMARK 500 ASP A 134 -90.65 -122.80 REMARK 500 TYR A 135 153.84 -22.05 REMARK 500 ASP A 161 -162.39 -121.65 REMARK 500 ALA A 245 63.41 -156.62 REMARK 500 ARG B 88 74.53 -150.16 REMARK 500 ARG B 102 146.29 169.88 REMARK 500 SER B 133 -143.09 52.50 REMARK 500 ASP B 134 21.35 110.63 REMARK 500 ASN B 154 32.28 -97.05 REMARK 500 ALA B 245 61.29 -152.77 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 CA A1287 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 140 OD2 REMARK 620 2 CYS A 186 O 84.8 REMARK 620 3 HOH A2045 O 73.6 67.8 REMARK 620 4 HOH A2087 O 97.4 107.2 169.8 REMARK 620 5 HOH A2088 O 166.8 82.1 99.8 87.9 REMARK 620 6 DC E 5 OP1 112.7 159.3 105.4 82.3 79.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B1287 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 140 OD2 REMARK 620 2 CYS B 186 O 91.1 REMARK 620 3 HOH B2041 O 84.2 73.9 REMARK 620 4 HOH B2060 O 85.7 105.5 169.9 REMARK 620 5 HOH B2074 O 171.8 83.1 99.6 90.2 REMARK 620 6 DC G 5 OP1 110.0 154.6 93.7 90.5 77.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA E1000 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH E2005 O REMARK 620 2 HOH E2005 O 113.3 REMARK 620 3 HOH E2006 O 72.3 71.0 REMARK 620 4 HOH E2006 O 71.0 72.3 110.2 REMARK 620 5 HOH E2014 O 147.8 84.3 89.9 141.1 REMARK 620 6 HOH E2014 O 84.3 147.9 141.1 89.9 94.4 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 CA A 1287 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 1287 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA E 1000 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FIU RELATED DB: PDB REMARK 900 TETRAMERIC RESTRICTION ENDONUCLEASE NGOMIV IN COMPLEX WITHCLEAVED REMARK 900 DNA DBREF 4ABT A 3 286 UNP P31032 T2M4_NEIGO 3 286 DBREF 4ABT B 3 286 UNP P31032 T2M4_NEIGO 3 286 DBREF 4ABT E 1 11 PDB 4ABT 4ABT 1 11 DBREF 4ABT G 1 11 PDB 4ABT 4ABT 1 11 SEQADV 4ABT MET A 1 UNP P31032 EXPRESSION TAG SEQADV 4ABT GLN A 2 UNP P31032 EXPRESSION TAG SEQADV 4ABT MET B 1 UNP P31032 EXPRESSION TAG SEQADV 4ABT GLN B 2 UNP P31032 EXPRESSION TAG SEQRES 1 A 286 MET GLN PRO LEU PHE THR GLN GLU ARG ARG ILE PHE HIS SEQRES 2 A 286 LYS LYS LEU LEU ASP GLY ASN ILE LEU ALA THR ASN ASN SEQRES 3 A 286 ARG GLY VAL VAL SER ASN ALA ASP GLY SER ASN THR ARG SEQRES 4 A 286 SER PHE ASN ILE ALA LYS GLY ILE ALA ASP LEU LEU HIS SEQRES 5 A 286 SER GLU THR VAL SER GLU ARG LEU PRO GLY GLN THR SER SEQRES 6 A 286 GLY ASN ALA PHE GLU ALA ILE CYS SER GLU PHE VAL GLN SEQRES 7 A 286 SER ALA PHE GLU LYS LEU GLN HIS ILE ARG PRO GLY ASP SEQRES 8 A 286 TRP ASN VAL LYS GLN VAL GLY SER ARG ASN ARG LEU GLU SEQRES 9 A 286 ILE ALA ARG TYR GLN GLN TYR ALA HIS LEU THR ALA LEU SEQRES 10 A 286 ALA LYS ALA ALA GLU GLU ASN PRO GLU LEU ALA ALA ALA SEQRES 11 A 286 LEU GLY SER ASP TYR THR ILE THR PRO ASP ILE ILE VAL SEQRES 12 A 286 THR ARG ASN LEU ILE ALA ASP ALA GLU ILE ASN ARG ASN SEQRES 13 A 286 GLU PHE LEU VAL ASP GLU ASN ILE ALA THR TYR ALA SER SEQRES 14 A 286 LEU ARG ALA GLY ASN GLY ASN MET PRO LEU LEU HIS ALA SEQRES 15 A 286 SER ILE SER CYS LYS TRP THR ILE ARG SER ASP ARG ALA SEQRES 16 A 286 GLN ASN ALA ARG SER GLU GLY LEU ASN LEU VAL ARG ASN SEQRES 17 A 286 ARG LYS GLY ARG LEU PRO HIS ILE VAL VAL VAL THR ALA SEQRES 18 A 286 GLU PRO THR PRO SER ARG ILE SER SER ILE ALA LEU GLY SEQRES 19 A 286 THR GLY GLU ILE ASP CYS VAL TYR HIS PHE ALA LEU TYR SEQRES 20 A 286 GLU LEU GLU GLN ILE LEU GLN SER LEU ASN TYR GLU ASP SEQRES 21 A 286 ALA LEU ASP LEU PHE TYR ILE MET VAL ASN GLY LYS ARG SEQRES 22 A 286 LEU LYS ASP ILE SER ASP LEU PRO LEU ASP LEU ALA VAL SEQRES 1 B 286 MET GLN PRO LEU PHE THR GLN GLU ARG ARG ILE PHE HIS SEQRES 2 B 286 LYS LYS LEU LEU ASP GLY ASN ILE LEU ALA THR ASN ASN SEQRES 3 B 286 ARG GLY VAL VAL SER ASN ALA ASP GLY SER ASN THR ARG SEQRES 4 B 286 SER PHE ASN ILE ALA LYS GLY ILE ALA ASP LEU LEU HIS SEQRES 5 B 286 SER GLU THR VAL SER GLU ARG LEU PRO GLY GLN THR SER SEQRES 6 B 286 GLY ASN ALA PHE GLU ALA ILE CYS SER GLU PHE VAL GLN SEQRES 7 B 286 SER ALA PHE GLU LYS LEU GLN HIS ILE ARG PRO GLY ASP SEQRES 8 B 286 TRP ASN VAL LYS GLN VAL GLY SER ARG ASN ARG LEU GLU SEQRES 9 B 286 ILE ALA ARG TYR GLN GLN TYR ALA HIS LEU THR ALA LEU SEQRES 10 B 286 ALA LYS ALA ALA GLU GLU ASN PRO GLU LEU ALA ALA ALA SEQRES 11 B 286 LEU GLY SER ASP TYR THR ILE THR PRO ASP ILE ILE VAL SEQRES 12 B 286 THR ARG ASN LEU ILE ALA ASP ALA GLU ILE ASN ARG ASN SEQRES 13 B 286 GLU PHE LEU VAL ASP GLU ASN ILE ALA THR TYR ALA SER SEQRES 14 B 286 LEU ARG ALA GLY ASN GLY ASN MET PRO LEU LEU HIS ALA SEQRES 15 B 286 SER ILE SER CYS LYS TRP THR ILE ARG SER ASP ARG ALA SEQRES 16 B 286 GLN ASN ALA ARG SER GLU GLY LEU ASN LEU VAL ARG ASN SEQRES 17 B 286 ARG LYS GLY ARG LEU PRO HIS ILE VAL VAL VAL THR ALA SEQRES 18 B 286 GLU PRO THR PRO SER ARG ILE SER SER ILE ALA LEU GLY SEQRES 19 B 286 THR GLY GLU ILE ASP CYS VAL TYR HIS PHE ALA LEU TYR SEQRES 20 B 286 GLU LEU GLU GLN ILE LEU GLN SER LEU ASN TYR GLU ASP SEQRES 21 B 286 ALA LEU ASP LEU PHE TYR ILE MET VAL ASN GLY LYS ARG SEQRES 22 B 286 LEU LYS ASP ILE SER ASP LEU PRO LEU ASP LEU ALA VAL SEQRES 1 E 11 DT DG DC DG DC DC DG DG DC DG DC SEQRES 1 G 11 DT DG DC DG DC DC DG DG DC DG DC HET CA A1287 1 HET CA B1287 1 HET CA E1000 1 HETNAM CA CALCIUM ION FORMUL 5 CA 3(CA 2+) FORMUL 8 HOH *246(H2 O) HELIX 1 1 PRO A 3 GLY A 19 1 17 HELIX 2 2 ASN A 37 LEU A 51 1 15 HELIX 3 3 PRO A 61 GLU A 82 1 22 HELIX 4 4 LYS A 83 GLN A 85 5 3 HELIX 5 5 GLU A 104 TYR A 108 5 5 HELIX 6 6 TYR A 108 TYR A 111 5 4 HELIX 7 7 ALA A 112 ASN A 124 1 13 HELIX 8 8 ASN A 124 GLY A 132 1 9 HELIX 9 9 ALA A 149 ASN A 154 1 6 HELIX 10 10 ASP A 193 ALA A 195 5 3 HELIX 11 11 GLN A 196 ARG A 209 1 14 HELIX 12 12 THR A 224 LEU A 233 1 10 HELIX 13 13 ALA A 245 LEU A 256 1 12 HELIX 14 14 TYR A 258 GLY A 271 1 14 HELIX 15 15 ASP A 279 LEU A 284 1 6 HELIX 16 16 PRO B 3 GLY B 19 1 17 HELIX 17 17 ASN B 37 LEU B 51 1 15 HELIX 18 18 PRO B 61 GLU B 82 1 22 HELIX 19 19 LEU B 103 TYR B 108 5 6 HELIX 20 20 TYR B 108 TYR B 111 5 4 HELIX 21 21 ALA B 112 ASN B 124 1 13 HELIX 22 22 ASN B 124 LEU B 131 1 8 HELIX 23 23 ALA B 149 ASN B 154 1 6 HELIX 24 24 ASP B 193 ALA B 195 5 3 HELIX 25 25 GLN B 196 ARG B 209 1 14 HELIX 26 26 THR B 224 LEU B 233 1 10 HELIX 27 27 ALA B 245 ASN B 257 1 13 HELIX 28 28 TYR B 258 GLY B 271 1 14 HELIX 29 29 ASP B 279 LEU B 284 1 6 SHEET 1 AA 6 ASP A 91 GLN A 96 0 SHEET 2 AA 6 ILE A 141 ASN A 146 -1 O ILE A 142 N LYS A 95 SHEET 3 AA 6 LEU A 179 LYS A 187 -1 O LEU A 179 N ARG A 145 SHEET 4 AA 6 HIS A 215 THR A 220 1 O HIS A 215 N SER A 183 SHEET 5 AA 6 CYS A 240 HIS A 243 1 O CYS A 240 N VAL A 218 SHEET 6 AA 6 LEU A 274 ASP A 276 1 O LYS A 275 N HIS A 243 SHEET 1 BA 6 TRP B 92 GLN B 96 0 SHEET 2 BA 6 ILE B 141 ARG B 145 -1 O ILE B 142 N LYS B 95 SHEET 3 BA 6 LEU B 179 LYS B 187 -1 O LEU B 179 N ARG B 145 SHEET 4 BA 6 HIS B 215 THR B 220 1 O HIS B 215 N SER B 183 SHEET 5 BA 6 CYS B 240 HIS B 243 1 O CYS B 240 N VAL B 218 SHEET 6 BA 6 LEU B 274 ASP B 276 1 O LYS B 275 N HIS B 243 LINK OD2 ASP A 140 CA CA A1287 1555 1555 2.37 LINK O CYS A 186 CA CA A1287 1555 1555 2.65 LINK CA CA A1287 O HOH A2045 1555 1555 2.80 LINK CA CA A1287 O HOH A2087 1555 1555 2.60 LINK CA CA A1287 O HOH A2088 1555 1555 2.33 LINK CA CA A1287 OP1 DC E 5 1555 1555 2.58 LINK OD2 ASP B 140 CA CA B1287 1555 1555 2.39 LINK O CYS B 186 CA CA B1287 1555 1555 2.47 LINK CA CA B1287 O HOH B2041 1555 1555 2.48 LINK CA CA B1287 O HOH B2060 1555 1555 2.53 LINK CA CA B1287 O HOH B2074 1555 1555 2.31 LINK CA CA B1287 OP1 DC G 5 1555 1555 2.33 LINK CA CA E1000 O HOH E2005 1555 2675 2.80 LINK CA CA E1000 O HOH E2005 1555 1555 2.79 LINK CA CA E1000 O HOH E2006 1555 1555 2.39 LINK CA CA E1000 O HOH E2006 1555 2675 2.39 LINK CA CA E1000 O HOH E2014 1555 1555 2.47 LINK CA CA E1000 O HOH E2014 1555 2675 2.47 SITE 1 AC1 6 ASP A 140 CYS A 186 HOH A2045 HOH A2087 SITE 2 AC1 6 HOH A2088 DC E 5 SITE 1 AC2 6 ASP B 140 CYS B 186 HOH B2041 HOH B2060 SITE 2 AC2 6 HOH B2074 DC G 5 SITE 1 AC3 3 HOH E2005 HOH E2006 HOH E2014 CRYST1 68.899 90.081 92.711 90.00 90.00 90.00 P 21 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 0.014514 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011101 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010786 0.00000