HEADER HYDROLASE/DNA 04-OCT-09 3K3R TITLE UNREFINED CRYSTAL STRUCTURE OF A LEXA-DNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEXA REPRESSOR; COMPND 3 CHAIN: E, F; COMPND 4 EC: 3.4.21.88; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (28-MER); COMPND 9 CHAIN: A, B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: LEXA, EXRA, SPR, TSL, UMUA, B4043, JW4003; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES KEYWDS PROTEIN-DNA COMPLEX, WINGED HELIX-TURN-HELIX, DOUBLE HELIX, KEYWDS 2 REPRESSOR, LEXA, SOS SYSTEM, AUTOCATALYTIC CLEAVAGE, DNA DAMAGE, DNA KEYWDS 3 REPAIR, DNA REPLICATION, DNA-BINDING, HYDROLASE, SOS RESPONSE, KEYWDS 4 TRANSCRIPTION, TRANSCRIPTION REGULATION, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION MDLTYP CA ATOMS ONLY, CHAIN E, F; P ATOMS ONLY, CHAIN A, B AUTHOR A.P.P.ZHANG,Y.Z.PIGLI,P.A.RICE REVDAT 5 21-FEB-24 3K3R 1 REMARK REVDAT 4 13-OCT-21 3K3R 1 SEQADV REVDAT 3 01-NOV-17 3K3R 1 REMARK REVDAT 2 19-JUN-13 3K3R 1 JRNL VERSN REVDAT 1 18-AUG-10 3K3R 0 JRNL AUTH A.P.ZHANG,Y.Z.PIGLI,P.A.RICE JRNL TITL STRUCTURE OF THE LEXA-DNA COMPLEX AND IMPLICATIONS FOR SOS JRNL TITL 2 BOX MEASUREMENT. JRNL REF NATURE V. 466 883 2010 JRNL REFN ISSN 0028-0836 JRNL PMID 20703307 JRNL DOI 10.1038/NATURE09200 REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 14447 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 347 REMARK 3 NUCLEIC ACID ATOMS : 56 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL 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 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THIS IS AN UNREFINED, CA/P ONLY, REMARK 3 PROTEIN/DNA CRYSTAL STRUCTURE REMARK 4 REMARK 4 3K3R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1000055508. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUL-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRROS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14447 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.12300 REMARK 200 FOR THE DATA SET : 13.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40MM TRIS-HCL, 1MM EDTA, 10MM MGCL2, REMARK 280 0.1M NACL, 5MM SPERMIDINE, 10% GLYCEROL, 12% (W/V) PEG5000, PH REMARK 280 8.5, HANGING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 22.67850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 74.90700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 60.19650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 74.90700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.67850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 60.19650 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 APPLY THE FOLLOWING TO CHAINS: E, F, 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 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 E 1 REMARK 465 GLU E 71 REMARK 465 GLU E 72 REMARK 465 GLU E 73 REMARK 465 GLU E 74 REMARK 465 GLY E 75 REMARK 465 LEU E 76 REMARK 465 PRO E 77 REMARK 465 LEU E 78 REMARK 465 VAL E 79 REMARK 465 GLY E 80 REMARK 465 ARG E 81 REMARK 465 VAL E 82 REMARK 465 ALA E 83 REMARK 465 ALA E 84 REMARK 465 GLY E 85 REMARK 465 GLU E 86 REMARK 465 PRO E 87 REMARK 465 LEU E 88 REMARK 465 LEU E 89 REMARK 465 ALA E 90 REMARK 465 GLN E 91 REMARK 465 GLN E 92 REMARK 465 HIS E 93 REMARK 465 ILE E 94 REMARK 465 ASP E 200 REMARK 465 TRP E 201 REMARK 465 LEU E 202 REMARK 465 MET F 1 REMARK 465 LYS F 2 REMARK 465 GLU F 71 REMARK 465 GLU F 72 REMARK 465 GLU F 73 REMARK 465 GLU F 74 REMARK 465 GLY F 75 REMARK 465 LEU F 76 REMARK 465 PRO F 77 REMARK 465 LEU F 78 REMARK 465 VAL F 79 REMARK 465 GLY F 80 REMARK 465 ARG F 81 REMARK 465 VAL F 82 REMARK 465 ALA F 83 REMARK 465 ALA F 84 REMARK 465 GLY F 85 REMARK 465 GLU F 86 REMARK 465 PRO F 87 REMARK 465 LEU F 88 REMARK 465 LEU F 89 REMARK 465 ALA F 90 REMARK 465 GLN F 91 REMARK 465 GLN F 92 REMARK 465 HIS F 93 REMARK 465 ILE F 94 REMARK 465 ASP F 200 REMARK 465 TRP F 201 REMARK 465 LEU F 202 REMARK 465 DG A 1 REMARK 465 DG B 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3JSO RELATED DB: PDB REMARK 900 SAME PROTEIN WITH A 22MER DNA CONTAINING AT-REPEATS IN THE SPACER REMARK 900 REGION REMARK 900 RELATED ID: 3JSP RELATED DB: PDB REMARK 900 SAME PROTEIN WITH A 22MER DNA CONTAINING GC-REPEATS IN THE SPACER REMARK 900 REGION DBREF 3K3R E 1 202 UNP P0A7C2 LEXA_ECOLI 1 202 DBREF 3K3R F 1 202 UNP P0A7C2 LEXA_ECOLI 1 202 DBREF 3K3R A 1 29 PDB 3K3R 3K3R 1 29 DBREF 3K3R B 1 29 PDB 3K3R 3K3R 1 29 SEQADV 3K3R ALA E 156 UNP P0A7C2 LYS 156 ENGINEERED MUTATION SEQADV 3K3R ALA F 156 UNP P0A7C2 LYS 156 ENGINEERED MUTATION SEQRES 1 E 202 MET LYS ALA LEU THR ALA ARG GLN GLN GLU VAL PHE ASP SEQRES 2 E 202 LEU ILE ARG ASP HIS ILE SER GLN THR GLY MET PRO PRO SEQRES 3 E 202 THR ARG ALA GLU ILE ALA GLN ARG LEU GLY PHE ARG SER SEQRES 4 E 202 PRO ASN ALA ALA GLU GLU HIS LEU LYS ALA LEU ALA ARG SEQRES 5 E 202 LYS GLY VAL ILE GLU ILE VAL SER GLY ALA SER ARG GLY SEQRES 6 E 202 ILE ARG LEU LEU GLN GLU GLU GLU GLU GLY LEU PRO LEU SEQRES 7 E 202 VAL GLY ARG VAL ALA ALA GLY GLU PRO LEU LEU ALA GLN SEQRES 8 E 202 GLN HIS ILE GLU GLY HIS TYR GLN VAL ASP PRO SER LEU SEQRES 9 E 202 PHE LYS PRO ASN ALA ASP PHE LEU LEU ARG VAL SER GLY SEQRES 10 E 202 MET SER MET LYS ASP ILE GLY ILE MET ASP GLY ASP LEU SEQRES 11 E 202 LEU ALA VAL HIS LYS THR GLN ASP VAL ARG ASN GLY GLN SEQRES 12 E 202 VAL VAL VAL ALA ARG ILE ASP ASP GLU VAL THR VAL ALA SEQRES 13 E 202 ARG LEU LYS LYS GLN GLY ASN LYS VAL GLU LEU LEU PRO SEQRES 14 E 202 GLU ASN SER GLU PHE LYS PRO ILE VAL VAL ASP LEU ARG SEQRES 15 E 202 GLN GLN SER PHE THR ILE GLU GLY LEU ALA VAL GLY VAL SEQRES 16 E 202 ILE ARG ASN GLY ASP TRP LEU SEQRES 1 F 202 MET LYS ALA LEU THR ALA ARG GLN GLN GLU VAL PHE ASP SEQRES 2 F 202 LEU ILE ARG ASP HIS ILE SER GLN THR GLY MET PRO PRO SEQRES 3 F 202 THR ARG ALA GLU ILE ALA GLN ARG LEU GLY PHE ARG SER SEQRES 4 F 202 PRO ASN ALA ALA GLU GLU HIS LEU LYS ALA LEU ALA ARG SEQRES 5 F 202 LYS GLY VAL ILE GLU ILE VAL SER GLY ALA SER ARG GLY SEQRES 6 F 202 ILE ARG LEU LEU GLN GLU GLU GLU GLU GLY LEU PRO LEU SEQRES 7 F 202 VAL GLY ARG VAL ALA ALA GLY GLU PRO LEU LEU ALA GLN SEQRES 8 F 202 GLN HIS ILE GLU GLY HIS TYR GLN VAL ASP PRO SER LEU SEQRES 9 F 202 PHE LYS PRO ASN ALA ASP PHE LEU LEU ARG VAL SER GLY SEQRES 10 F 202 MET SER MET LYS ASP ILE GLY ILE MET ASP GLY ASP LEU SEQRES 11 F 202 LEU ALA VAL HIS LYS THR GLN ASP VAL ARG ASN GLY GLN SEQRES 12 F 202 VAL VAL VAL ALA ARG ILE ASP ASP GLU VAL THR VAL ALA SEQRES 13 F 202 ARG LEU LYS LYS GLN GLY ASN LYS VAL GLU LEU LEU PRO SEQRES 14 F 202 GLU ASN SER GLU PHE LYS PRO ILE VAL VAL ASP LEU ARG SEQRES 15 F 202 GLN GLN SER PHE THR ILE GLU GLY LEU ALA VAL GLY VAL SEQRES 16 F 202 ILE ARG ASN GLY ASP TRP LEU SEQRES 1 A 29 DG DT DT DG DA DT DA DC DT DG DT DA DT SEQRES 2 A 29 DG DA DT DC DA DT DA DC DA DG DT DA DT SEQRES 3 A 29 DC DA DA SEQRES 1 B 29 DG DT DT DG DA DT DA DC DT DG DT DA DT SEQRES 2 B 29 DG DA DT DC DA DT DA DC DA DG DT DA DT SEQRES 3 B 29 DC DA DA CRYST1 45.357 120.393 149.814 90.00 90.00 90.00 P 21 21 21 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 0.022047 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008306 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006675 0.00000