HEADER DNA BINDING PROTEIN/DNA 02-NOV-14 4WUL TITLE CRYSTAL STRUCTURE OF E. FAECALIS DNA BINDING DOMAIN LIARD191N TITLE 2 COMPLEXED WITH 26BP DNA CAVEAT 4WUL RESIDUE H DA -101 AND RESIDUE H DA -100 ARE NOT PROPERLY CAVEAT 2 4WUL LINKED: DISTANCE BETWEEN O3' AND P IS 8.98 A COMPND MOL_ID: 1; COMPND 2 MOLECULE: RESPONSE REGULATOR RECEIVER DOMAIN PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: DNA BINDING DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (26-MER); COMPND 8 CHAIN: H; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA (26-MER); COMPND 12 CHAIN: C; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 3 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 4 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 6 EXPRESSION_SYSTEM_PLASMID: PETDUET; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: ENTEROCOCCUS FAECALIS S613; SOURCE 10 ORGANISM_TAXID: 699185; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: ENTEROCOCCUS FAECALIS S613; SOURCE 14 ORGANISM_TAXID: 699185 KEYWDS HELIX-TURN-HELIX, RESPONSE REGULATOR, ENTEROCOCCI, DNA BINDING KEYWDS 2 DOMAIN, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.DAVLIEVA,Y.SHAMOO REVDAT 5 11-DEC-19 4WUL 1 REMARK REVDAT 4 20-SEP-17 4WUL 1 REMARK REVDAT 3 26-AUG-15 4WUL 1 REMARK REVDAT 2 03-JUN-15 4WUL 1 JRNL REVDAT 1 06-MAY-15 4WUL 0 JRNL AUTH M.DAVLIEVA,Y.SHI,P.G.LEONARD,T.A.JOHNSON,M.R.ZIANNI, JRNL AUTH 2 C.A.ARIAS,J.E.LADBURY,Y.SHAMOO JRNL TITL A VARIABLE DNA RECOGNITION SITE ORGANIZATION ESTABLISHES THE JRNL TITL 2 LIAR-MEDIATED CELL ENVELOPE STRESS RESPONSE OF ENTEROCOCCI JRNL TITL 3 TO DAPTOMYCIN. JRNL REF NUCLEIC ACIDS RES. V. 43 4758 2015 JRNL REFN ESSN 1362-4962 JRNL PMID 25897118 JRNL DOI 10.1093/NAR/GKV321 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 13364 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.980 REMARK 3 FREE R VALUE TEST SET COUNT : 1334 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 29.4468 - 5.2515 1.00 1252 145 0.2081 0.2286 REMARK 3 2 5.2515 - 4.1721 1.00 1222 134 0.1959 0.2149 REMARK 3 3 4.1721 - 3.6458 1.00 1205 131 0.1880 0.2914 REMARK 3 4 3.6458 - 3.3130 1.00 1206 134 0.2038 0.2654 REMARK 3 5 3.3130 - 3.0758 1.00 1196 128 0.2121 0.3323 REMARK 3 6 3.0758 - 2.8946 1.00 1206 133 0.2742 0.3531 REMARK 3 7 2.8946 - 2.7497 1.00 1203 133 0.2809 0.3045 REMARK 3 8 2.7497 - 2.6301 1.00 1187 130 0.2481 0.3256 REMARK 3 9 2.6301 - 2.5289 1.00 1180 131 0.2535 0.2789 REMARK 3 10 2.5289 - 2.4417 0.98 1173 135 0.2600 0.3240 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.130 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.96 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.004 2229 REMARK 3 ANGLE : 0.686 3233 REMARK 3 CHIRALITY : 0.026 378 REMARK 3 PLANARITY : 0.002 231 REMARK 3 DIHEDRAL : 25.205 890 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 3.3254 42.4077 -9.1498 REMARK 3 T TENSOR REMARK 3 T11: 0.1416 T22: 0.2190 REMARK 3 T33: 0.2422 T12: 0.0183 REMARK 3 T13: 0.2302 T23: 0.0329 REMARK 3 L TENSOR REMARK 3 L11: 0.0366 L22: 0.0445 REMARK 3 L33: 0.0717 L12: -0.0069 REMARK 3 L13: 0.0216 L23: -0.0204 REMARK 3 S TENSOR REMARK 3 S11: 0.1086 S12: 0.0188 S13: -0.0214 REMARK 3 S21: 0.0013 S22: 0.0990 S23: -0.0034 REMARK 3 S31: -0.0215 S32: 0.0085 S33: 0.1602 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4WUL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-NOV-14. REMARK 100 THE DEPOSITION ID IS D_1000204532. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : KOHZU REMARK 200 OPTICS : BIMORPH K-B PAIR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 22.50 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : 0.10100 REMARK 200 FOR THE DATA SET : 33.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 22.30 REMARK 200 R MERGE FOR SHELL (I) : 0.73300 REMARK 200 R SYM FOR SHELL (I) : 0.73300 REMARK 200 FOR SHELL : 9.333 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: 4WTO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.08 M KCL, 0.02 M BACL2, 0.04 M REMARK 280 SODIUM CACODYLATE (PH 6.0), 43% MPD, 0.012 M SPERMINE REMARK 280 TETRACHLORIDE, 0.01 M PROLINE, 0.01 M STRONTIUM CHLORIDE, PH 8.6, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 283K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.15000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 16.07500 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 32.15000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 16.07500 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: A, B, H, 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 139 REMARK 465 VAL A 140 REMARK 465 LYS A 206 REMARK 465 MET B 139 REMARK 465 VAL B 140 REMARK 465 LEU B 141 REMARK 465 LYS B 206 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 B 306 O HOH B 307 1.90 REMARK 500 O HOH H 114 O HOH H 125 2.02 REMARK 500 O HOH A 307 O HOH H 106 2.06 REMARK 500 O HOH A 308 O HOH A 309 2.08 REMARK 500 OP2 DG H -103 O HOH H 133 2.11 REMARK 500 N7 DA H -102 O HOH H 128 2.12 REMARK 500 OP2 DT C -124 O HOH C 101 2.13 REMARK 500 O HOH H 118 O HOH H 120 2.14 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 DT H-116 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT C-124 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4WUH RELATED DB: PDB REMARK 900 RELATED ID: 4WU4 RELATED DB: PDB REMARK 900 RELATED ID: 4WT0 RELATED DB: PDB REMARK 900 RELATED ID: 4WSZ RELATED DB: PDB DBREF 4WUL A 140 206 UNP R3G073 R3G073_ENTFL 144 210 DBREF 4WUL B 140 206 UNP R3G073 R3G073_ENTFL 144 210 DBREF 4WUL H -124 -99 PDB 4WUL 4WUL -124 -99 DBREF 4WUL C -99 -124 PDB 4WUL 4WUL -99 -124 SEQADV 4WUL MET A 139 UNP R3G073 INITIATING METHIONINE SEQADV 4WUL ASN A 191 UNP R3G073 ASP 195 CONFLICT SEQADV 4WUL MET B 139 UNP R3G073 INITIATING METHIONINE SEQADV 4WUL ASN B 191 UNP R3G073 ASP 195 CONFLICT SEQRES 1 A 68 MET VAL LEU HIS GLU ASP LEU THR ASN ARG GLU HIS GLU SEQRES 2 A 68 ILE LEU MET LEU ILE ALA GLN GLY LYS SER ASN GLN GLU SEQRES 3 A 68 ILE ALA ASP GLU LEU PHE ILE THR LEU LYS THR VAL LYS SEQRES 4 A 68 THR HIS VAL SER ASN ILE LEU ALA LYS LEU ASP VAL ASP SEQRES 5 A 68 ASN ARG THR GLN ALA ALA ILE TYR ALA PHE GLN HIS GLY SEQRES 6 A 68 LEU ALA LYS SEQRES 1 B 68 MET VAL LEU HIS GLU ASP LEU THR ASN ARG GLU HIS GLU SEQRES 2 B 68 ILE LEU MET LEU ILE ALA GLN GLY LYS SER ASN GLN GLU SEQRES 3 B 68 ILE ALA ASP GLU LEU PHE ILE THR LEU LYS THR VAL LYS SEQRES 4 B 68 THR HIS VAL SER ASN ILE LEU ALA LYS LEU ASP VAL ASP SEQRES 5 B 68 ASN ARG THR GLN ALA ALA ILE TYR ALA PHE GLN HIS GLY SEQRES 6 B 68 LEU ALA LYS SEQRES 1 H 26 DA DC DT DA DG DT DC DC DT DT DA DC DT SEQRES 2 H 26 DA DA DT DG DA DG DA DA DG DA DA DA DT SEQRES 1 C 26 DA DT DT DT DC DT DT DC DT DC DA DT DT SEQRES 2 C 26 DA DG DT DA DA DG DG DA DC DT DA DG DT FORMUL 5 HOH *98(H2 O) HELIX 1 AA1 THR A 146 ALA A 157 1 12 HELIX 2 AA2 SER A 161 PHE A 170 1 10 HELIX 3 AA3 THR A 172 ASP A 188 1 17 HELIX 4 AA4 ASN A 191 HIS A 202 1 12 HELIX 5 AA5 THR B 146 ALA B 157 1 12 HELIX 6 AA6 SER B 161 PHE B 170 1 10 HELIX 7 AA7 THR B 172 ASP B 188 1 17 HELIX 8 AA8 ASN B 191 HIS B 202 1 12 CISPEP 1 HIS B 142 GLU B 143 0 0.91 CRYST1 113.585 113.585 48.225 90.00 90.00 120.00 P 62 12 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 0.008804 0.005083 0.000000 0.00000 SCALE2 0.000000 0.010166 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020736 0.00000 MASTER 278 0 0 8 0 0 0 6 0 0 0 16 END