HEADER HYDROLASE/DNA 09-DEC-15 5F8A TITLE CRYSTAL STRUCTURE OF THE TERNARY ECORV-DNA-LU COMPLEX WITH UNCLEAVED TITLE 2 DNA SUBSTRATE. LANTHANIDE BINDING TO ECORV-DNA COMPLEX INHIBITS TITLE 3 CLEAVAGE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*AP*AP*AP*GP*AP*TP*AP*TP*CP*TP*TP*T)-3'); COMPND 3 CHAIN: C, D; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: TYPE-2 RESTRICTION ENZYME ECORV; COMPND 7 CHAIN: A, B; COMPND 8 SYNONYM: R.ECORV,ENDONUCLEASE ECORV,TYPE II RESTRICTION ENZYME ECORV; COMPND 9 EC: 3.1.21.4; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 7 ORGANISM_TAXID: 562; SOURCE 8 GENE: ECORVR; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE, PROTEIN-DNA COMPLEX, LUTETIUM, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.S.SANGANI,A.D.KEHR,K.SINHA,G.S.RULE,L.JEN-JACOBSON REVDAT 5 27-SEP-23 5F8A 1 LINK REVDAT 4 25-DEC-19 5F8A 1 REMARK REVDAT 3 27-SEP-17 5F8A 1 REMARK REVDAT 2 21-DEC-16 5F8A 1 JRNL REVDAT 1 09-NOV-16 5F8A 0 JRNL AUTH K.SINHA,S.S.SANGANI,A.D.KEHR,G.S.RULE,L.JEN-JACOBSON JRNL TITL METAL ION BINDING AT THE CATALYTIC SITE INDUCES WIDELY JRNL TITL 2 DISTRIBUTED CHANGES IN A SEQUENCE SPECIFIC PROTEIN-DNA JRNL TITL 3 COMPLEX. JRNL REF BIOCHEMISTRY V. 55 6115 2016 JRNL REFN ISSN 1520-4995 JRNL PMID 27786446 JRNL DOI 10.1021/ACS.BIOCHEM.6B00919 REMARK 2 REMARK 2 RESOLUTION. 1.76 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 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) : 1.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.67 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 3 NUMBER OF REFLECTIONS : 46685 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) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.700 REMARK 3 FREE R VALUE TEST SET COUNT : 5000 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) : 1.76 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.81 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3227 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.06 REMARK 3 BIN R VALUE (WORKING SET) : 0.2620 REMARK 3 BIN FREE R VALUE SET COUNT : 366 REMARK 3 BIN FREE R VALUE : 0.3150 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4046 REMARK 3 NUCLEIC ACID ATOMS : 486 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 301 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.87 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.96000 REMARK 3 B22 (A**2) : 1.36000 REMARK 3 B33 (A**2) : -1.83000 REMARK 3 B12 (A**2) : -0.78000 REMARK 3 B13 (A**2) : 0.85000 REMARK 3 B23 (A**2) : -0.66000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.127 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.120 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.078 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.494 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.955 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4732 ; 0.017 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): 4326 ; 0.007 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6507 ; 1.574 ; 1.848 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9845 ; 1.056 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 496 ; 6.598 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 214 ;38.752 ;24.299 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 743 ;14.434 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;20.122 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 668 ; 0.103 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5018 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1116 ; 0.002 ; 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): 1963 ; 2.672 ; 2.496 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1962 ; 2.666 ; 2.495 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2454 ; 3.520 ; 3.729 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2455 ; 3.521 ; 3.729 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2769 ; 3.806 ; 2.865 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2770 ; 3.806 ; 2.865 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4050 ; 5.393 ; 4.151 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5898 ; 6.468 ;21.722 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5896 ; 6.468 ;21.718 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 5F8A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-DEC-15. REMARK 100 THE DEPOSITION ID IS D_1000216066. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-NOV-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 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 FR-E DW REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS HTC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM 7.2.1 REMARK 200 DATA SCALING SOFTWARE : SCALA CCP4INTERFACE 6.5.019 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51697 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.760 REMARK 200 RESOLUTION RANGE LOW (A) : 36.673 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : 0.05900 REMARK 200 FOR THE DATA SET : 14.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.76 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.19600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER CCP4INTERFACE 6.5.019 REMARK 200 STARTING MODEL: 1B95 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4.5 MG/ML (MONOMER), REMARK 280 PROTEIN(DIMER):DNA - 1:1, ENZYME:WELL - 3UL:3UL, WELL - 500UL OF REMARK 280 100 MM HEPES PH 7.4, 8% ETHYLENE GLYCOL, 4% POLYETHYLENE GLYCOL REMARK 280 8000, 10% GLYCEROL., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 285K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: 9970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, 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 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 LU LU B 301 O HOH B 464 1.94 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 DA C 2 O3' DA C 2 C3' -0.037 REMARK 500 GLU A 45 CD GLU A 45 OE1 -0.101 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 C 5 O5' - P - OP2 ANGL. DEV. = 7.4 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 85 65.90 -119.47 REMARK 500 SER A 112 -112.40 -100.71 REMARK 500 PRO A 162 30.94 -83.75 REMARK 500 LYS A 229 -86.13 -130.47 REMARK 500 LYS B 85 67.00 -119.80 REMARK 500 SER B 112 -113.16 -101.23 REMARK 500 LYS B 229 -88.47 -138.38 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 NA A 302 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 15 O REMARK 620 2 TYR A 18 O 95.1 REMARK 620 3 ASP A 19 OD1 154.0 91.2 REMARK 620 4 EDO A 303 O1 100.5 90.4 104.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 LU A 301 LU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 45 OE1 REMARK 620 2 GLU A 45 OE2 47.0 REMARK 620 3 ASP A 74 OD1 83.9 129.6 REMARK 620 4 ASP A 74 OD2 72.1 92.9 55.3 REMARK 620 5 HOH A 409 O 112.6 77.7 121.9 76.7 REMARK 620 6 HOH A 422 O 150.0 152.3 68.7 82.1 74.6 REMARK 620 7 HOH A 441 O 70.1 94.9 73.9 118.5 163.8 111.4 REMARK 620 8 HOH A 484 O 109.1 76.4 142.8 161.4 86.1 100.2 78.1 REMARK 620 9 HOH A 523 O 137.5 145.1 76.7 122.0 109.7 48.6 68.4 70.4 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 302 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN B 15 O REMARK 620 2 TYR B 18 O 99.8 REMARK 620 3 ASP B 19 OD1 143.5 86.3 REMARK 620 4 EDO B 303 O2 100.9 91.1 115.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 LU B 301 LU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 45 OE1 REMARK 620 2 GLU B 45 OE2 51.3 REMARK 620 3 ASP B 74 OD1 89.8 127.8 REMARK 620 4 ASP B 74 OD2 81.7 83.9 53.6 REMARK 620 5 HOH B 410 O 121.2 72.6 116.0 75.6 REMARK 620 6 HOH B 459 O 69.6 111.3 76.3 121.9 161.9 REMARK 620 7 HOH B 488 O 95.8 76.6 149.8 156.6 86.2 77.9 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 LU A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LU B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 303 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4ORJ RELATED DB: PDB REMARK 900 4ORJ IS THE SAME PROTEIN-DNA COMPLEX WHERE THE DNA IS CLEAVED REMARK 900 RELATED ID: 5HLK RELATED DB: PDB DBREF 5F8A C 1 12 PDB 5F8A 5F8A 1 12 DBREF 5F8A D 1 12 PDB 5F8A 5F8A 1 12 DBREF 5F8A A 2 245 UNP P04390 T2E5_ECOLX 2 245 DBREF 5F8A B 2 245 UNP P04390 T2E5_ECOLX 2 245 SEQRES 1 C 12 DA DA DA DG DA DT DA DT DC DT DT DT SEQRES 1 D 12 DA DA DA DG DA DT DA DT DC DT DT DT SEQRES 1 A 244 SER LEU ARG SER ASP LEU ILE ASN ALA LEU TYR ASP GLU SEQRES 2 A 244 ASN GLN LYS TYR ASP VAL CYS GLY ILE ILE SER ALA GLU SEQRES 3 A 244 GLY LYS ILE TYR PRO LEU GLY SER ASP THR LYS VAL LEU SEQRES 4 A 244 SER THR ILE PHE GLU LEU PHE SER ARG PRO ILE ILE ASN SEQRES 5 A 244 LYS ILE ALA GLU LYS HIS GLY TYR ILE VAL GLU GLU PRO SEQRES 6 A 244 LYS GLN GLN ASN HIS TYR PRO ASP PHE THR LEU TYR LYS SEQRES 7 A 244 PRO SER GLU PRO ASN LYS LYS ILE ALA ILE ASP ILE LYS SEQRES 8 A 244 THR THR TYR THR ASN LYS GLU ASN GLU LYS ILE LYS PHE SEQRES 9 A 244 THR LEU GLY GLY TYR THR SER PHE ILE ARG ASN ASN THR SEQRES 10 A 244 LYS ASN ILE VAL TYR PRO PHE ASP GLN TYR ILE ALA HIS SEQRES 11 A 244 TRP ILE ILE GLY TYR VAL TYR THR ARG VAL ALA THR ARG SEQRES 12 A 244 LYS SER SER LEU LYS THR TYR ASN ILE ASN GLU LEU ASN SEQRES 13 A 244 GLU ILE PRO LYS PRO TYR LYS GLY VAL LYS VAL PHE LEU SEQRES 14 A 244 GLN ASP LYS TRP VAL ILE ALA GLY ASP LEU ALA GLY SER SEQRES 15 A 244 GLY ASN THR THR ASN ILE GLY SER ILE HIS ALA HIS TYR SEQRES 16 A 244 LYS ASP PHE VAL GLU GLY LYS GLY ILE PHE ASP SER GLU SEQRES 17 A 244 ASP GLU PHE LEU ASP TYR TRP ARG ASN TYR GLU ARG THR SEQRES 18 A 244 SER GLN LEU ARG ASN ASP LYS TYR ASN ASN ILE SER GLU SEQRES 19 A 244 TYR ARG ASN TRP ILE TYR ARG GLY ARG LYS SEQRES 1 B 244 SER LEU ARG SER ASP LEU ILE ASN ALA LEU TYR ASP GLU SEQRES 2 B 244 ASN GLN LYS TYR ASP VAL CYS GLY ILE ILE SER ALA GLU SEQRES 3 B 244 GLY LYS ILE TYR PRO LEU GLY SER ASP THR LYS VAL LEU SEQRES 4 B 244 SER THR ILE PHE GLU LEU PHE SER ARG PRO ILE ILE ASN SEQRES 5 B 244 LYS ILE ALA GLU LYS HIS GLY TYR ILE VAL GLU GLU PRO SEQRES 6 B 244 LYS GLN GLN ASN HIS TYR PRO ASP PHE THR LEU TYR LYS SEQRES 7 B 244 PRO SER GLU PRO ASN LYS LYS ILE ALA ILE ASP ILE LYS SEQRES 8 B 244 THR THR TYR THR ASN LYS GLU ASN GLU LYS ILE LYS PHE SEQRES 9 B 244 THR LEU GLY GLY TYR THR SER PHE ILE ARG ASN ASN THR SEQRES 10 B 244 LYS ASN ILE VAL TYR PRO PHE ASP GLN TYR ILE ALA HIS SEQRES 11 B 244 TRP ILE ILE GLY TYR VAL TYR THR ARG VAL ALA THR ARG SEQRES 12 B 244 LYS SER SER LEU LYS THR TYR ASN ILE ASN GLU LEU ASN SEQRES 13 B 244 GLU ILE PRO LYS PRO TYR LYS GLY VAL LYS VAL PHE LEU SEQRES 14 B 244 GLN ASP LYS TRP VAL ILE ALA GLY ASP LEU ALA GLY SER SEQRES 15 B 244 GLY ASN THR THR ASN ILE GLY SER ILE HIS ALA HIS TYR SEQRES 16 B 244 LYS ASP PHE VAL GLU GLY LYS GLY ILE PHE ASP SER GLU SEQRES 17 B 244 ASP GLU PHE LEU ASP TYR TRP ARG ASN TYR GLU ARG THR SEQRES 18 B 244 SER GLN LEU ARG ASN ASP LYS TYR ASN ASN ILE SER GLU SEQRES 19 B 244 TYR ARG ASN TRP ILE TYR ARG GLY ARG LYS HET LU A 301 1 HET NA A 302 1 HET EDO A 303 4 HET LU B 301 1 HET NA B 302 1 HET EDO B 303 4 HETNAM LU LUTETIUM (III) ION HETNAM NA SODIUM ION HETNAM EDO 1,2-ETHANEDIOL HETSYN LU LU HETSYN EDO ETHYLENE GLYCOL FORMUL 5 LU 2(LU 3+) FORMUL 6 NA 2(NA 1+) FORMUL 7 EDO 2(C2 H6 O2) FORMUL 11 HOH *301(H2 O) HELIX 1 AA1 SER A 2 TYR A 18 1 17 HELIX 2 AA2 ASP A 36 HIS A 59 1 24 HELIX 3 AA3 PRO A 124 ASP A 126 5 3 HELIX 4 AA4 ARG A 144 LYS A 149 5 6 HELIX 5 AA5 ASN A 152 ILE A 159 5 8 HELIX 6 AA6 LYS A 173 ALA A 177 1 5 HELIX 7 AA7 HIS A 195 GLY A 202 1 8 HELIX 8 AA8 SER A 208 ASN A 218 1 11 HELIX 9 AA9 THR A 222 ASP A 228 1 7 HELIX 10 AB1 ASN A 232 ARG A 242 1 11 HELIX 11 AB2 LEU B 3 TYR B 18 1 16 HELIX 12 AB3 ASP B 36 HIS B 59 1 24 HELIX 13 AB4 PRO B 124 ASP B 126 5 3 HELIX 14 AB5 ARG B 144 LYS B 149 5 6 HELIX 15 AB6 ASN B 152 ILE B 159 5 8 HELIX 16 AB7 LYS B 173 ALA B 177 1 5 HELIX 17 AB8 HIS B 195 GLY B 202 1 8 HELIX 18 AB9 SER B 208 ASN B 218 1 11 HELIX 19 AC1 THR B 222 ASN B 227 1 6 HELIX 20 AC2 ASN B 232 ARG B 242 1 11 SHEET 1 AA1 4 ILE A 30 PRO A 32 0 SHEET 2 AA1 4 VAL A 20 SER A 25 -1 N ILE A 23 O TYR A 31 SHEET 3 AA1 4 VAL B 20 SER B 25 -1 O ILE B 24 N GLY A 22 SHEET 4 AA1 4 ILE B 30 PRO B 32 -1 O TYR B 31 N ILE B 23 SHEET 1 AA2 5 ILE A 62 GLU A 64 0 SHEET 2 AA2 5 PHE A 75 LYS A 79 -1 O TYR A 78 N ILE A 62 SHEET 3 AA2 5 GLU A 82 THR A 96 -1 O ILE A 87 N LEU A 77 SHEET 4 AA2 5 TYR A 128 ARG A 140 1 O TRP A 132 N ALA A 88 SHEET 5 AA2 5 TYR A 163 ASP A 172 -1 O GLN A 171 N ILE A 133 SHEET 1 AA3 2 THR A 106 GLY A 109 0 SHEET 2 AA3 2 ASN A 188 GLY A 190 -1 O ILE A 189 N GLY A 108 SHEET 1 AA4 5 ILE B 62 GLU B 64 0 SHEET 2 AA4 5 PHE B 75 TYR B 78 -1 O TYR B 78 N ILE B 62 SHEET 3 AA4 5 LYS B 86 THR B 96 -1 O ILE B 89 N PHE B 75 SHEET 4 AA4 5 TYR B 128 ARG B 140 1 O TRP B 132 N ALA B 88 SHEET 5 AA4 5 TYR B 163 ASP B 172 -1 O GLN B 171 N ILE B 133 SHEET 1 AA5 2 THR B 106 GLY B 109 0 SHEET 2 AA5 2 ASN B 188 GLY B 190 -1 O ILE B 189 N GLY B 108 LINK O ASN A 15 NA NA A 302 1555 1555 2.23 LINK O TYR A 18 NA NA A 302 1555 1555 2.40 LINK OD1 ASP A 19 NA NA A 302 1555 1555 2.28 LINK OE1 GLU A 45 LU LU A 301 1555 1555 2.67 LINK OE2 GLU A 45 LU LU A 301 1555 1555 2.30 LINK OD1 ASP A 74 LU LU A 301 1555 1555 2.27 LINK OD2 ASP A 74 LU LU A 301 1555 1555 2.40 LINK LU LU A 301 O HOH A 409 1555 1555 2.26 LINK LU LU A 301 O HOH A 422 1555 1555 3.05 LINK LU LU A 301 O HOH A 441 1555 1555 2.24 LINK LU LU A 301 O HOH A 484 1555 1555 2.28 LINK LU LU A 301 O HOH A 523 1555 1555 2.68 LINK NA NA A 302 O1 EDO A 303 1555 1555 2.25 LINK O ASN B 15 NA NA B 302 1555 1555 2.20 LINK O TYR B 18 NA NA B 302 1555 1555 2.34 LINK OD1 ASP B 19 NA NA B 302 1555 1555 2.34 LINK OE1 GLU B 45 LU LU B 301 1555 1555 2.60 LINK OE2 GLU B 45 LU LU B 301 1555 1555 2.33 LINK OD1 ASP B 74 LU LU B 301 1555 1555 2.30 LINK OD2 ASP B 74 LU LU B 301 1555 1555 2.50 LINK LU LU B 301 O HOH B 410 1555 1555 2.33 LINK LU LU B 301 O HOH B 459 1555 1555 2.27 LINK LU LU B 301 O HOH B 488 1555 1555 2.41 LINK NA NA B 302 O2 EDO B 303 1555 1555 2.31 CISPEP 1 TYR A 72 PRO A 73 0 -6.86 CISPEP 2 TYR B 72 PRO B 73 0 -2.65 SITE 1 AC1 7 GLU A 45 ASP A 74 HOH A 409 HOH A 422 SITE 2 AC1 7 HOH A 441 HOH A 484 HOH A 523 SITE 1 AC2 4 ASN A 15 TYR A 18 ASP A 19 EDO A 303 SITE 1 AC3 7 ASN A 15 TYR A 18 ASP A 19 VAL A 20 SITE 2 AC3 7 PHE A 44 PHE A 47 NA A 302 SITE 1 AC4 6 GLU B 45 ASP B 74 HOH B 410 HOH B 459 SITE 2 AC4 6 HOH B 464 HOH B 488 SITE 1 AC5 4 ASN B 15 TYR B 18 ASP B 19 EDO B 303 SITE 1 AC6 5 ASN B 15 TYR B 18 ASP B 19 VAL B 20 SITE 2 AC6 5 NA B 302 CRYST1 46.430 52.860 65.310 70.61 73.24 81.81 P 1 2 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 0.021538 -0.003100 -0.005816 0.00000 SCALE2 0.000000 0.019113 -0.006164 0.00000 SCALE3 0.000000 0.000000 0.016802 0.00000