PDB Short entry for 3ZDB HEADER HYDROLASE/DNA 26-NOV-12 3ZDB TITLE STRUCTURE OF E. COLI EXOIX IN COMPLEX WITH THE PALINDROMIC 5OV4 DNA TITLE 2 OLIGONUCLEOTIDE, DI-MAGNESIUM 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: 5OV4 DNA, 5'-D(*AP*AP*AP*AP*GP*CP*GP*TP*AP*CP*GP*CP)-3'; COMPND 9 CHAIN: X; COMPND 10 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_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PJONEX; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PCI857; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 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 01-MAY-24 3ZDB 1 REMARK LINK REVDAT 3 09-OCT-13 3ZDB 1 JRNL REVDAT 2 17-JUL-13 3ZDB 1 JRNL REVDAT 1 10-JUL-13 3ZDB 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. 1.47 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.47 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.67 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 57465 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) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3074 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) : 1.47 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.51 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4169 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.55 REMARK 3 BIN R VALUE (WORKING SET) : 0.3160 REMARK 3 BIN FREE R VALUE SET COUNT : 225 REMARK 3 BIN FREE R VALUE : 0.3580 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1906 REMARK 3 NUCLEIC ACID ATOMS : 245 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 203 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.74 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.30000 REMARK 3 B22 (A**2) : 0.18000 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): 0.068 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.070 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.041 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.037 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2243 ; 0.013 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1429 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3101 ; 1.440 ; 2.096 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3497 ; 0.919 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 248 ; 5.351 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 89 ;41.843 ;23.820 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 321 ;11.812 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;14.275 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 347 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2329 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 412 ; 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): 1236 ;18.583 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 494 ; 4.593 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1981 ;18.783 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1007 ;37.768 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1118 ;37.366 ; 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 3ZDB 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_1290054863. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-MAR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 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 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60541 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.470 REMARK 200 RESOLUTION RANGE LOW (A) : 33.670 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 6.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.47 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.24000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.700 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 (%): 60.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM ACETATE, 15% (W/V) PEG REMARK 280 -3350, PH 6.5 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 33.11900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 76.15100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.11900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 76.15100 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: 4810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -86.2 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, X 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 ARG A 54 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 SER A 55 OG REMARK 470 ASN A 206 CG OD1 ND2 REMARK 470 LEU A 207 CG CD1 CD2 REMARK 470 ASP A 208 CG OD1 OD2 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 GLU A 219 CG CD OE1 OE2 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 LEU A 194 O PHE A 197 2.02 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 DA X 2 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DT X 8 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DC X 10 O4' - C1' - N1 ANGL. DEV. = 4.6 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 ASN A 206 67.63 -119.50 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 A1253 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 104 OD1 REMARK 620 2 ASP A 104 OD2 51.3 REMARK 620 3 HOH A2010 O 90.5 108.0 REMARK 620 4 HOH A2011 O 100.5 56.4 83.5 REMARK 620 5 HOH A2046 O 88.0 138.1 77.9 159.6 REMARK 620 6 HOH A2066 O 88.1 68.1 175.8 92.9 106.0 REMARK 620 7 HOH A2196 O 165.9 135.6 97.0 92.2 81.9 85.1 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 79.3 REMARK 620 3 PRO A 180 O 90.7 88.6 REMARK 620 4 VAL A 182 O 70.7 149.9 94.5 REMARK 620 5 ILE A 185 O 74.8 87.1 165.3 82.4 REMARK 620 6 MG A1252 MG 124.1 56.3 117.5 142.4 71.1 REMARK 620 7 HOH A2148 O 142.5 67.9 71.5 141.1 119.4 48.8 REMARK 620 8 DC X 10 OP2 141.6 95.0 127.4 106.4 67.0 38.8 62.0 REMARK 620 N 1 2 3 4 5 6 7 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 ALA A 172 O REMARK 620 2 ILE A 185 O 98.6 REMARK 620 3 HOH A2148 O 89.2 169.4 REMARK 620 4 HOH A2149 O 76.2 98.7 90.1 REMARK 620 5 HOH A2151 O 97.3 89.1 82.7 170.4 REMARK 620 6 DC X 10 OP2 159.4 84.4 90.8 83.2 103.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1255 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2009 O REMARK 620 2 HOH A2010 O 79.8 REMARK 620 3 HOH A2045 O 96.0 93.8 REMARK 620 4 HOH A2046 O 158.7 87.6 102.0 REMARK 620 5 HOH A2196 O 73.2 87.8 168.6 89.4 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 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 MG A 1255 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1253 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT 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: 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 OLIGO DESIGNED BASED ON INITIAL STRUCTURE WITH FRAGMENT OF REMARK 999 LARGER DNA DBREF 3ZDB A 1 251 UNP Q8X6R9 XNI_ECO57 1 251 DBREF 3ZDB X 1 12 PDB 3ZDB 3ZDB 1 12 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 X 12 DA DA DA DA DG DC DG DT DA DC DG DC HET K A1251 1 HET MG A1252 1 HET MG A1253 1 HET ACT A1254 4 HET MG A1255 1 HETNAM K POTASSIUM ION HETNAM MG MAGNESIUM ION HETNAM ACT ACETATE ION FORMUL 3 K K 1+ FORMUL 4 MG 3(MG 2+) FORMUL 6 ACT C2 H3 O2 1- FORMUL 8 HOH *203(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 A1253 1555 1555 2.11 LINK OD2 ASP A 104 MG MG A1253 1555 1555 2.80 LINK O LEU A 171 K K A1251 1555 1555 3.40 LINK O ALA A 172 K K A1251 1555 1555 2.67 LINK O ALA A 172 MG MG A1252 1555 1555 2.22 LINK O PRO A 180 K K A1251 1555 1555 3.13 LINK O VAL A 182 K K A1251 1555 1555 2.88 LINK O ILE A 185 K K A1251 1555 1555 2.45 LINK O ILE A 185 MG MG A1252 1555 1555 2.43 LINK K K A1251 MG MG A1252 1555 1555 1.53 LINK K K A1251 O HOH A2148 1555 1555 2.97 LINK K K A1251 OP2 DC X 10 1555 1555 2.87 LINK MG MG A1252 O HOH A2148 1555 1555 2.28 LINK MG MG A1252 O HOH A2149 1555 1555 2.19 LINK MG MG A1252 O HOH A2151 1555 1555 2.02 LINK MG MG A1252 OP2 DC X 10 1555 1555 1.93 LINK MG MG A1253 O HOH A2010 1555 1555 1.87 LINK MG MG A1253 O HOH A2011 1555 1555 2.09 LINK MG MG A1253 O HOH A2046 1555 1555 2.43 LINK MG MG A1253 O HOH A2066 1555 1555 2.09 LINK MG MG A1253 O HOH A2196 1555 1555 2.04 LINK MG MG A1255 O HOH A2009 1555 1555 2.01 LINK MG MG A1255 O HOH A2010 1555 1555 2.00 LINK MG MG A1255 O HOH A2045 1555 1555 2.06 LINK MG MG A1255 O HOH A2046 1555 1555 1.96 LINK MG MG A1255 O HOH A2196 1555 1555 2.22 CISPEP 1 SER A 23 PRO A 24 0 -0.17 SITE 1 AC1 8 LEU A 171 ALA A 172 PRO A 180 VAL A 182 SITE 2 AC1 8 ILE A 185 MG A1252 HOH A2148 DC X 10 SITE 1 AC2 7 ALA A 172 ILE A 185 K A1251 HOH A2148 SITE 2 AC2 7 HOH A2149 HOH A2151 DC X 10 SITE 1 AC3 6 MG A1253 HOH A2009 HOH A2010 HOH A2045 SITE 2 AC3 6 HOH A2046 HOH A2196 SITE 1 AC4 7 ASP A 104 MG A1255 HOH A2010 HOH A2011 SITE 2 AC4 7 HOH A2046 HOH A2066 HOH A2196 SITE 1 AC5 6 GLN A 35 LEU A 36 ARG A 141 LYS A 146 SITE 2 AC5 6 HOH A2032 HOH A2094 CRYST1 66.238 152.302 34.522 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 0.015097 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006566 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028967 0.00000