HEADER HYDROLASE/DNA 26-NOV-12 3ZDA TITLE STRUCTURE OF E. COLI EXOIX IN COMPLEX WITH A FRAGMENT OF THE FLAP1 DNA TITLE 2 OLIGONUCLEOTIDE, POTASSIUM AND MAGNESIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN XNI; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: EXOIX; COMPND 5 EC: 3.1.-.-; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-D(*GP*CP*GP*CP)-3'; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: FLAP1 FRAGMENT; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: 5'-D(*AP*AP*GP*CP*GP*CP)-3'; COMPND 14 CHAIN: C; COMPND 15 SYNONYM: FLAP1 FRAGMENT; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 STRAIN: XL-1 BLUE; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: PCI857; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PJONEX; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630 KEYWDS HYDROLASE-DNA COMPLEX, FLAP ENDONUCLEASE, DNA BINDING EXPDTA X-RAY DIFFRACTION AUTHOR G.R.HEMSWORTH,C.S.ANSTEY-GILBERT,C.S.FLEMMING,M.R.G.HODSKINSON, AUTHOR 2 J.ZHANG,S.E.SEDELNIKOVA,T.J.STILLMAN,J.R.SAYERS,P.J.ARTYMIUK REVDAT 4 30-OCT-19 3ZDA 1 REMARK LINK REVDAT 3 09-OCT-13 3ZDA 1 JRNL REVDAT 2 17-JUL-13 3ZDA 1 JRNL REVDAT 1 10-JUL-13 3ZDA 0 JRNL AUTH C.S.ANSTEY-GILBERT,G.R.HEMSWORTH,C.S.FLEMMING, JRNL AUTH 2 M.R.G.HODSKINSON,J.ZHANG,S.E.SEDELNIKOVA,T.J.STILLMAN, JRNL AUTH 3 J.R.SAYERS,P.J.ARTYMIUK JRNL TITL THE STRUCTURE OF E. COLI EXOIX - IMPLICATIONS FOR DNA JRNL TITL 2 BINDING AND CATALYSIS IN FLAP ENDONUCLEASES JRNL REF NUCLEIC ACIDS RES. V. 41 8357 2013 JRNL REFN ISSN 0305-1048 JRNL PMID 23821668 JRNL DOI 10.1093/NAR/GKT591 REMARK 2 REMARK 2 RESOLUTION. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.64 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 54940 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) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2950 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3938 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.81 REMARK 3 BIN R VALUE (WORKING SET) : 0.3320 REMARK 3 BIN FREE R VALUE SET COUNT : 219 REMARK 3 BIN FREE R VALUE : 0.3360 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1915 REMARK 3 NUCLEIC ACID ATOMS : 206 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 243 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.20000 REMARK 3 B22 (A**2) : 0.71000 REMARK 3 B33 (A**2) : -0.51000 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): 0.074 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.075 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.051 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.333 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2199 ; 0.015 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1407 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3028 ; 1.547 ; 2.079 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3444 ; 0.939 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 245 ; 5.410 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 87 ;40.619 ;23.908 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 322 ;12.439 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;14.858 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 340 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2291 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 403 ; 0.001 ; 0.020 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): 1232 ;16.331 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 494 ; 5.001 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1975 ;14.774 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 967 ;38.204 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1053 ;35.483 ; 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. REMARK 4 REMARK 4 3ZDA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-NOV-12. REMARK 100 THE DEPOSITION ID IS D_1290054862. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-DEC-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 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) : 0.976 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57905 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 51.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 6.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.900 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.5000 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) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.48000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3ZD9 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM ACETATE, 15% (W/V) PEG REMARK 280 -3350, PH 6.0 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 33.10150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 77.41000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.10150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 77.41000 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.4 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 MET A 1 REMARK 465 GLU A 52 REMARK 465 ASN A 53 REMARK 465 ARG A 251 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 51 CG OD1 OD2 REMARK 470 ARG A 54 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 75 CG CD OE1 OE2 REMARK 470 GLU A 157 CG CD OE1 OE2 REMARK 470 ASN A 206 CG OD1 ND2 REMARK 470 GLU A 212 CG CD OE1 OE2 REMARK 470 ARG A 215 CG CD NE CZ NH1 NH2 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 ND1 HIS A 239 O HOH A 2225 2.07 REMARK 500 O HOH A 2074 O HOH A 2157 2.07 REMARK 500 O HOH A 2156 O HOH A 2157 2.11 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 P DG B 1 O3' DC C 16 2555 1.83 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 29 CB CYS A 29 SG -0.122 REMARK 500 DC C 16 O3' DC C 16 C3' -0.041 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 ASP A 9 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 DG B 3 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC B 4 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DA C 11 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DA C 11 C3' - O3' - P ANGL. DEV. = 8.1 DEGREES REMARK 500 DA C 12 C3' - O3' - P ANGL. DEV. = 8.0 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 LEU A 171 -62.83 -90.68 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 A1252 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 104 OD1 REMARK 620 2 ASP A 104 OD2 49.0 REMARK 620 3 HOH A2098 O 85.6 66.4 REMARK 620 4 HOH A2077 O 90.3 139.2 115.5 REMARK 620 5 HOH A2240 O 171.7 123.3 93.4 97.5 REMARK 620 6 HOH A2019 O 98.4 54.6 88.1 155.5 73.3 REMARK 620 7 HOH A2017 O 81.8 97.5 163.8 74.8 97.6 83.8 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A1251 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 171 O REMARK 620 2 ALA A 172 O 76.4 REMARK 620 3 PRO A 180 O 89.4 85.9 REMARK 620 4 VAL A 182 O 73.7 149.6 99.4 REMARK 620 5 ILE A 185 O 73.8 88.3 163.1 78.0 REMARK 620 6 DC B 2 OP1 147.4 127.8 111.5 78.2 84.5 REMARK 620 7 HOH A2194 O 144.5 86.4 58.2 122.0 137.2 66.2 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 1251 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1252 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PIV A 1253 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 1254 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ZD8 RELATED DB: PDB REMARK 900 POTASSIUM BOUND STRUCTURE OF E. COLI EXOIX IN P1 REMARK 900 RELATED ID: 3ZD9 RELATED DB: PDB REMARK 900 POTASSIUM BOUND STRUCTURE OF E. COLI EXOIX IN P21 REMARK 900 RELATED ID: 3ZDB RELATED DB: PDB REMARK 900 STRUCTURE OF E. COLI EXOIX IN COMPLEX WITH THE PALINDROMIC 5OV4 DNA REMARK 900 OLIGONUCLEOTIDE, DI-MAGNESIUM AND POTASSIUM REMARK 900 RELATED ID: 3ZDC RELATED DB: PDB REMARK 900 STRUCTURE OF E. COLI EXOIX IN COMPLEX WITH THE PALINDROMIC 5OV4 DNA REMARK 900 OLIGONUCLEOTIDE, POTASSIUM AND CALCIUM REMARK 900 RELATED ID: 3ZDD RELATED DB: PDB REMARK 900 STRUCTURE OF E. COLI EXOIX IN COMPLEX WITH THE PALINDROMIC 5OV6 REMARK 900 OLIGONUCLEOTIDE AND POTASSIUM REMARK 900 RELATED ID: 3ZDE RELATED DB: PDB REMARK 900 POTASSIUM FREE STRUCTURE OF E. COLI EXOIX REMARK 999 REMARK 999 SEQUENCE REMARK 999 FRAGMENT OF LARGER DNA BOUND TO PROTEIN. SEQUENCE IS REMARK 999 ACTUALLY UNKNOWN, CRYSTAL LIKELY HAS MIXED DNAS BOUND HERE. DBREF 3ZDA A 1 251 UNP Q8X6R9 XNI_ECO57 1 251 DBREF 3ZDA B 1 4 PDB 3ZDA 3ZDA 1 4 DBREF 3ZDA C 11 16 PDB 3ZDA 3ZDA 11 16 SEQRES 1 A 251 MET ALA VAL HIS LEU LEU ILE VAL ASP ALA LEU ASN LEU SEQRES 2 A 251 ILE ARG ARG ILE HIS ALA VAL GLN GLY SER PRO CYS VAL SEQRES 3 A 251 GLU THR CYS GLN HIS ALA LEU ASP GLN LEU ILE MET HIS SEQRES 4 A 251 SER GLN PRO THR HIS ALA VAL ALA VAL PHE ASP ASP GLU SEQRES 5 A 251 ASN ARG SER SER GLY TRP ARG HIS GLN ARG LEU PRO ASP SEQRES 6 A 251 TYR LYS ALA GLY ARG PRO PRO MET PRO GLU GLU LEU HIS SEQRES 7 A 251 ASP GLU MET PRO ALA LEU ARG ALA ALA PHE GLU GLN ARG SEQRES 8 A 251 GLY VAL PRO CYS TRP SER THR SER GLY ASN GLU ALA ASP SEQRES 9 A 251 ASP LEU ALA ALA THR LEU ALA VAL LYS VAL THR GLN ALA SEQRES 10 A 251 GLY HIS GLN ALA THR ILE VAL SER THR ASP LYS GLY TYR SEQRES 11 A 251 CYS GLN LEU LEU SER PRO THR LEU ARG ILE ARG ASP TYR SEQRES 12 A 251 PHE GLN LYS ARG TRP LEU ASP ALA PRO PHE ILE ASP LYS SEQRES 13 A 251 GLU PHE GLY VAL GLN PRO GLN GLN LEU PRO ASP TYR TRP SEQRES 14 A 251 GLY LEU ALA GLY ILE SER SER SER LYS VAL PRO GLY VAL SEQRES 15 A 251 ALA GLY ILE GLY PRO LYS SER ALA THR GLN LEU LEU VAL SEQRES 16 A 251 GLU PHE GLN SER LEU GLU GLY ILE TYR GLU ASN LEU ASP SEQRES 17 A 251 ALA VAL ALA GLU LYS TRP ARG LYS LYS LEU GLU THR HIS SEQRES 18 A 251 LYS GLU MET ALA PHE LEU CYS ARG ASP ILE ALA ARG LEU SEQRES 19 A 251 GLN THR ASP LEU HIS ILE ASP GLY ASN LEU GLN GLN LEU SEQRES 20 A 251 ARG LEU VAL ARG SEQRES 1 B 4 DG DC DG DC SEQRES 1 C 6 DA DA DG DC DG DC HET K A1251 1 HET MG A1252 1 HET PIV A1253 7 HET PO4 A1254 5 HETNAM K POTASSIUM ION HETNAM MG MAGNESIUM ION HETNAM PIV PIVALIC ACID HETNAM PO4 PHOSPHATE ION FORMUL 4 K K 1+ FORMUL 5 MG MG 2+ FORMUL 6 PIV C5 H10 O2 FORMUL 7 PO4 O4 P 3- FORMUL 8 HOH *243(H2 O) HELIX 1 1 ALA A 10 GLY A 22 1 13 HELIX 2 2 CYS A 25 GLN A 41 1 17 HELIX 3 3 GLY A 57 LEU A 63 1 7 HELIX 4 4 PRO A 74 GLY A 92 1 19 HELIX 5 5 GLU A 102 ALA A 117 1 16 HELIX 6 6 ASP A 127 LEU A 134 5 8 HELIX 7 7 ASP A 150 GLY A 159 1 10 HELIX 8 8 GLN A 161 GLN A 163 5 3 HELIX 9 9 GLN A 164 GLY A 173 1 10 HELIX 10 10 SER A 175 LYS A 178 5 4 HELIX 11 11 GLY A 186 PHE A 197 1 12 HELIX 12 12 SER A 199 ASN A 206 1 8 HELIX 13 13 LEU A 207 VAL A 210 5 4 HELIX 14 14 ALA A 211 HIS A 221 1 11 HELIX 15 15 HIS A 221 ARG A 233 1 13 HELIX 16 16 ASN A 243 LEU A 247 5 5 SHEET 1 AA 6 CYS A 95 THR A 98 0 SHEET 2 AA 6 HIS A 44 ASP A 50 1 O ALA A 47 N TRP A 96 SHEET 3 AA 6 HIS A 4 ASP A 9 1 O HIS A 4 N HIS A 44 SHEET 4 AA 6 GLN A 120 VAL A 124 1 O GLN A 120 N LEU A 5 SHEET 5 AA 6 LEU A 138 ASP A 142 1 O ARG A 139 N ILE A 123 SHEET 6 AA 6 ARG A 147 TRP A 148 -1 O ARG A 147 N ASP A 142 LINK OD1 ASP A 104 MG MG A1252 1555 1555 2.09 LINK OD2 ASP A 104 MG MG A1252 1555 1555 2.94 LINK O LEU A 171 K K A1251 1555 1555 3.25 LINK O ALA A 172 K K A1251 1555 1555 2.82 LINK O PRO A 180 K K A1251 1555 1555 2.86 LINK O VAL A 182 K K A1251 1555 1555 2.68 LINK O ILE A 185 K K A1251 1555 1555 2.56 LINK OP1 DC B 2 K K A1251 1555 1555 3.28 LINK K K A1251 O HOH A2194 1555 1555 3.00 LINK MG MG A1252 O HOH A2098 1555 1555 2.34 LINK MG MG A1252 O HOH A2077 1555 1555 2.39 LINK MG MG A1252 O HOH A2240 1555 1555 2.03 LINK MG MG A1252 O HOH A2019 1555 1555 2.38 LINK MG MG A1252 O HOH A2017 1555 1555 2.00 CISPEP 1 SER A 23 PRO A 24 0 -1.71 SITE 1 AC1 7 LEU A 171 ALA A 172 PRO A 180 VAL A 182 SITE 2 AC1 7 ILE A 185 HOH A2194 DC B 2 SITE 1 AC2 6 ASP A 104 HOH A2017 HOH A2019 HOH A2077 SITE 2 AC2 6 HOH A2098 HOH A2240 SITE 1 AC3 9 GLN A 35 LEU A 36 HIS A 39 ARG A 141 SITE 2 AC3 9 TYR A 143 LYS A 146 HOH A2056 HOH A2061 SITE 3 AC3 9 HOH A2125 SITE 1 AC4 6 LEU A 110 LYS A 113 ILE A 240 LEU A 244 SITE 2 AC4 6 HOH A2231 HOH A2241 CRYST1 66.203 154.820 34.473 90.00 90.00 90.00 P 21 21 2 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 0.015105 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006459 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029008 0.00000 MASTER 422 0 4 16 6 0 9 6 0 0 0 22 END