HEADER HYDROLASE/DNA 26-NOV-12 3ZDD TITLE STRUCTURE OF E. COLI EXOIX IN COMPLEX WITH THE PALINDROMIC 5OV6 TITLE 2 OLIGONUCLEOTIDE AND POTASSIUM 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: 5OV6 DNA; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: 5'-D(*TP*GP*GP*CP*GP*TP*AP*CP*GP*CP)-3'; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 STRAIN: XL1 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_PLASMID: PJONEX; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630 KEYWDS HYDROLASE-DNA COMPLEX, ENDONUCLEASE, DNA BINDING EXPDTA X-RAY DIFFRACTION AUTHOR C.S.FLEMMING,G.R.HEMSWORTH,C.S.ANSTEY-GILBERT,M.R.G.HODSKINSON, AUTHOR 2 J.ZHANG,S.E.SEDELNIKOVA,T.J.STILLMAN,J.R.SAYERS,P.J.ARTYMIUK REVDAT 5 01-MAY-24 3ZDD 1 REMARK LINK REVDAT 4 20-FEB-19 3ZDD 1 SOURCE JRNL REVDAT 3 09-OCT-13 3ZDD 1 JRNL REVDAT 2 17-JUL-13 3ZDD 1 JRNL REVDAT 1 10-JUL-13 3ZDD 0 JRNL AUTH C.S.ANSTEY-GILBERT,G.R.HEMSWORTH,C.S.FLEMMING, JRNL AUTH 2 M.R.HODSKINSON,J.ZHANG,S.E.SEDELNIKOVA,T.J.STILLMAN, JRNL AUTH 3 J.R.SAYERS,P.J.ARTYMIUK JRNL TITL THE STRUCTURE OF ESCHERICHIA COLI EXOIX--IMPLICATIONS FOR JRNL TITL 2 DNA BINDING AND CATALYSIS IN FLAP ENDONUCLEASES. JRNL REF NUCLEIC ACIDS RES. V. 41 8357 2013 JRNL REFN ESSN 1362-4962 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 5.6.0117 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) : 30.34 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 51998 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) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2783 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) : 3464 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.62 REMARK 3 BIN R VALUE (WORKING SET) : 0.3320 REMARK 3 BIN FREE R VALUE SET COUNT : 199 REMARK 3 BIN FREE R VALUE : 0.3840 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1920 REMARK 3 NUCLEIC ACID ATOMS : 206 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 220 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.59 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.62000 REMARK 3 B22 (A**2) : 1.06000 REMARK 3 B33 (A**2) : -0.45000 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): 0.080 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.084 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.063 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.694 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.930 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2242 ; 0.018 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1452 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3091 ; 1.624 ; 2.074 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3550 ; 0.974 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 254 ; 5.337 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 94 ;39.833 ;23.830 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 332 ;12.985 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;18.250 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 344 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2358 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 418 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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. U VALUES REFINED INDIVIDUALLY REMARK 4 REMARK 4 3ZDD 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_1290054865. 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 REMARK 200 PH : 7.5 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) : 0.980 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54849 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 31.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 6.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.6000 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) : 1.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.52000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: EXOIX FLAP1 FRAGMENT COMPLEX STRUCTURE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.5, 10 % ISOPROPANOL, REMARK 280 20% PEG 4000 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 33.17950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 75.00150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.17950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 75.00150 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.9 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 SER A 99 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 54 CG CD NE CZ NH1 NH2 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 470 LYS A 216 CG CD CE NZ REMARK 470 VAL A 250 CG1 CG2 REMARK 470 ARG A 251 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 O HOH A 2138 O HOH A 2139 1.94 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 237 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 DG B 7 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC B 9 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG B 14 C3' - C2' - C1' ANGL. DEV. = -5.2 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 GLN A 198 -52.79 78.55 REMARK 500 ASN A 206 44.91 -164.44 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 K A1252 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 171 O REMARK 620 2 ALA A 172 O 80.1 REMARK 620 3 PRO A 180 O 90.5 85.7 REMARK 620 4 VAL A 182 O 75.3 155.3 97.1 REMARK 620 5 ILE A 185 O 74.1 91.4 164.6 79.5 REMARK 620 6 HOH A2167 O 137.8 115.3 54.6 85.4 139.0 REMARK 620 7 DC B 13 OP1 149.9 125.4 105.9 77.6 88.2 51.3 REMARK 620 8 DC B 13 OP2 144.9 79.6 116.1 119.9 78.0 77.1 46.9 REMARK 620 N 1 2 3 4 5 6 7 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 1252 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IPA A 1253 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO 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: 3ZDA RELATED DB: PDB REMARK 900 STRUCTURE OF E. COLI EXOIX IN COMPLEX WITH A FRAGMENT OF THE FLAP1 REMARK 900 DNA OLIGOCULEOTIDE, POTASSIUM AND MAGNESIUM 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: 3ZDE RELATED DB: PDB REMARK 900 POTASSIUM FREE STRUCTURE OF E. COLI EXOIX REMARK 999 REMARK 999 SEQUENCE REMARK 999 OLIGO DESIGNED BASED ON INITIAL STRUCTURE WITH FRAGMENT OF REMARK 999 LARGER DNA.THE GENBACK REFERENCE PROVIDED BY AUTHOR FOR REMARK 999 CHAIN A IS ZP_02776037.1 DBREF 3ZDD A 1 251 UNP Q8X6R9 XNI_ECO57 1 251 DBREF 3ZDD B 6 15 PDB 3ZDD 3ZDD 6 15 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 10 DT DG DG DC DG DT DA DC DG DC HET K A1252 1 HET IPA A1253 4 HET EDO A1254 4 HETNAM K POTASSIUM ION HETNAM IPA ISOPROPYL ALCOHOL HETNAM EDO 1,2-ETHANEDIOL HETSYN IPA 2-PROPANOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 K K 1+ FORMUL 4 IPA C3 H8 O FORMUL 5 EDO C2 H6 O2 FORMUL 6 HOH *220(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 GLN A 198 1 13 HELIX 12 12 SER A 199 GLU A 205 1 7 HELIX 13 13 ASN A 206 VAL A 210 5 5 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 TRP A 96 0 SHEET 2 AA 6 HIS A 44 VAL A 48 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 O LEU A 171 K K A1252 1555 1555 3.04 LINK O ALA A 172 K K A1252 1555 1555 2.92 LINK O PRO A 180 K K A1252 1555 1555 2.88 LINK O VAL A 182 K K A1252 1555 1555 2.78 LINK O ILE A 185 K K A1252 1555 1555 2.49 LINK K K A1252 O HOH A2167 1555 1555 3.39 LINK K K A1252 OP1 DC B 13 1555 1555 3.12 LINK K K A1252 OP2 DC B 13 1555 1555 3.27 CISPEP 1 SER A 23 PRO A 24 0 1.39 SITE 1 AC1 6 LEU A 171 ALA A 172 PRO A 180 VAL A 182 SITE 2 AC1 6 ILE A 185 DC B 13 SITE 1 AC2 1 VAL A 114 SITE 1 AC3 5 LYS A 156 PHE A 226 ARG A 229 ASP A 230 SITE 2 AC3 5 HOH A2213 CRYST1 66.359 150.003 34.228 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 0.015070 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006667 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029216 0.00000