HEADER DNA BINDING PROTEIN 18-DEC-20 7BBQ TITLE CRYSTAL STRUCTURE OF THE HTH DNA BINDING PROTEIN ARDK FROM R388 TITLE 2 PLASMID. APO FORM. COMPND MOL_ID: 1; COMPND 2 MOLECULE: KORA DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET29C KEYWDS DNA BINDING PROTEIN, HELIX TURN HELIX, DIRECT REPEAT, PLASMID KEYWDS 2 CONJUGATION EXPDTA X-RAY DIFFRACTION AUTHOR R.FERNANDEZ-LOPEZ,D.R.BOER,G.MONCALIAN REVDAT 3 14-DEC-22 7BBQ 1 JRNL REVDAT 2 23-NOV-22 7BBQ 1 JRNL REVDAT 1 13-JUL-22 7BBQ 0 JRNL AUTH R.FERNANDEZ-LOPEZ,R.RUIZ,I.DEL CAMPO,L.GONZALEZ-MONTES, JRNL AUTH 2 D.R.BOER,F.DE LA CRUZ,G.MONCALIAN JRNL TITL STRUCTURAL BASIS OF DIRECT AND INVERTED DNA SEQUENCE REPEAT JRNL TITL 2 RECOGNITION BY HELIX-TURN-HELIX TRANSCRIPTION FACTORS. JRNL REF NUCLEIC ACIDS RES. V. 50 11938 2022 JRNL REFN ESSN 1362-4962 JRNL PMID 36370103 JRNL DOI 10.1093/NAR/GKAC1024 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 4047 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.248 REMARK 3 R VALUE (WORKING SET) : 0.246 REMARK 3 FREE R VALUE : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.460 REMARK 3 FREE R VALUE TEST SET COUNT : 221 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 30.1000 - 3.7800 0.99 1960 134 0.2174 0.2419 REMARK 3 2 3.7800 - 3.0000 1.00 1866 87 0.3404 0.4244 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) : 0.343 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.037 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 96.07 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 86.77 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 : 0.013 742 REMARK 3 ANGLE : 1.442 1001 REMARK 3 CHIRALITY : 0.071 115 REMARK 3 PLANARITY : 0.007 133 REMARK 3 DIHEDRAL : 25.507 103 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 7BBQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1292110831. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-APR-07 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM16 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM 7.2.2 REMARK 200 DATA SCALING SOFTWARE : SCALA CCP4 7.0.078 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4103 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 63.630 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.09700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.16 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.37100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX 1.17.1_3660 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM TRIS-HCL, 150 MM NACL, 1 MM REMARK 280 EDTA, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 95.44500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 21.55000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 21.55000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 47.72250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 21.55000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 21.55000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 143.16750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 21.55000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 21.55000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 47.72250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 21.55000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 21.55000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 143.16750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 95.44500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 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 MSE A 1 REMARK 465 THR A 2 REMARK 465 ALA A 3 REMARK 465 ALA A 4 REMARK 465 ALA A 5 REMARK 465 PHE A 6 REMARK 465 ASP A 7 REMARK 465 ASP A 8 REMARK 465 LEU A 9 REMARK 465 ARG A 10 REMARK 465 PRO A 11 REMARK 465 ARG A 12 REMARK 465 HIS A 107 REMARK 465 HIS A 108 REMARK 465 HIS A 109 REMARK 465 HIS A 110 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 LEU A 13 CG CD1 CD2 REMARK 470 HIS A 106 CG ND1 CD2 CE1 NE2 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 GLU A 30 81.10 53.16 REMARK 500 GLU A 104 46.31 -101.20 REMARK 500 HIS A 105 -141.84 68.86 REMARK 500 REMARK 500 REMARK: NULL DBREF 7BBQ A 1 102 UNP Q6I6B7 Q6I6B7_ECOLX 6 107 SEQADV 7BBQ LEU A 98 UNP Q6I6B7 SER 103 ENGINEERED MUTATION SEQADV 7BBQ LEU A 103 UNP Q6I6B7 EXPRESSION TAG SEQADV 7BBQ GLU A 104 UNP Q6I6B7 EXPRESSION TAG SEQADV 7BBQ HIS A 105 UNP Q6I6B7 EXPRESSION TAG SEQADV 7BBQ HIS A 106 UNP Q6I6B7 EXPRESSION TAG SEQADV 7BBQ HIS A 107 UNP Q6I6B7 EXPRESSION TAG SEQADV 7BBQ HIS A 108 UNP Q6I6B7 EXPRESSION TAG SEQADV 7BBQ HIS A 109 UNP Q6I6B7 EXPRESSION TAG SEQADV 7BBQ HIS A 110 UNP Q6I6B7 EXPRESSION TAG SEQRES 1 A 110 MSE THR ALA ALA ALA PHE ASP ASP LEU ARG PRO ARG LEU SEQRES 2 A 110 GLY ARG LEU THR GLU GLU THR ILE ASP ILE ALA ARG GLU SEQRES 3 A 110 VAL LEU VAL GLU GLY LYS SER GLN SER ASP VAL ALA ARG SEQRES 4 A 110 GLU ARG GLY LEU SER ARG GLN ARG VAL SER SER MSE VAL SEQRES 5 A 110 LYS SER VAL VAL SER ALA ALA ASN GLU ILE PRO ARG GLU SEQRES 6 A 110 TRP GLN ARG VAL GLU VAL TRP LEU PRO PRO ASN LEU ALA SEQRES 7 A 110 GLU LYS VAL ARG GLN MSE GLU ALA ASP ALA LYS ALA ASP SEQRES 8 A 110 VAL ALA ARG LYS ASN GLN LEU THR ASP ALA ALA LEU GLU SEQRES 9 A 110 HIS HIS HIS HIS HIS HIS MODRES 7BBQ MSE A 51 MET MODIFIED RESIDUE MODRES 7BBQ MSE A 84 MET MODIFIED RESIDUE HET MSE A 51 8 HET MSE A 84 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 2(C5 H11 N O2 SE) HELIX 1 AA1 THR A 17 VAL A 29 1 13 HELIX 2 AA2 SER A 33 GLY A 42 1 10 HELIX 3 AA3 SER A 44 SER A 57 1 14 HELIX 4 AA4 ASN A 76 LEU A 103 1 28 LINK C SER A 50 N MSE A 51 1555 1555 1.34 LINK C MSE A 51 N VAL A 52 1555 1555 1.34 LINK C GLN A 83 N MSE A 84 1555 1555 1.35 LINK C MSE A 84 N GLU A 85 1555 1555 1.34 CRYST1 43.100 43.100 190.890 90.00 90.00 90.00 P 41 21 2 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 0.023202 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023202 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005239 0.00000