HEADER DNA BINDING PROTEIN 11-FEB-20 6LXL TITLE CRYSTAL STRUCTURE OF C-TERMINAL DNA-BINDING DOMAIN OF ESCHERICHIA COLI TITLE 2 OMPR COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REGULATORY PROTEIN OMPR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: OMPR, NCTC10764_03768; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS DNA BINDING PROTEIN TRANSCRIPTION FACTOR, TRANSCRIPTION, DNA BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.SADOTRA,C.CHEN,C.H.HSU REVDAT 2 29-NOV-23 6LXL 1 REMARK REVDAT 1 23-DEC-20 6LXL 0 JRNL AUTH S.SADOTRA,Y.C.LOU,H.C.TANG,Y.C.CHIU,C.H.HSU,C.CHEN JRNL TITL STRUCTURAL BASIS FOR PROMOTER DNA RECOGNITION BY THE JRNL TITL 2 RESPONSE REGULATOR OMPR. JRNL REF J.STRUCT.BIOL. V. 213 07638 2020 JRNL REFN ESSN 1095-8657 JRNL PMID 33152421 JRNL DOI 10.1016/J.JSB.2020.107638 REMARK 2 REMARK 2 RESOLUTION. 3.56 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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 : CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.56 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 72.3 REMARK 3 NUMBER OF REFLECTIONS : 2548 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.242 REMARK 3 R VALUE (WORKING SET) : 0.234 REMARK 3 FREE R VALUE : 0.319 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.690 REMARK 3 FREE R VALUE TEST SET COUNT : 247 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 29.8800 - 4.4800 0.89 1424 149 0.2365 0.3181 REMARK 3 2 4.4800 - 3.5600 0.55 877 98 0.2298 0.3196 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) : 0.466 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.235 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.92 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 : 0.003 740 REMARK 3 ANGLE : 0.542 999 REMARK 3 CHIRALITY : 0.040 110 REMARK 3 PLANARITY : 0.003 129 REMARK 3 DIHEDRAL : 2.159 454 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 6LXL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1300014867. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-DEC-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL13C1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.975 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2548 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.560 REMARK 200 RESOLUTION RANGE LOW (A) : 29.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.400 REMARK 200 R MERGE (I) : 0.17500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.56 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.69 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4NHJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CHES PH 9.5 10% PEG 3000, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 288K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 41.87400 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 30.14850 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 30.14850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 62.81100 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 30.14850 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 30.14850 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 20.93700 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 30.14850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.14850 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 62.81100 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 30.14850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 30.14850 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 20.93700 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 41.87400 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: MONOMERIC 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 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 ARG A 56 REMARK 465 GLY A 57 REMARK 465 ARG A 58 REMARK 465 GLU A 59 REMARK 465 TYR A 60 REMARK 465 SER A 61 REMARK 465 ALA A 62 REMARK 465 MET A 63 REMARK 465 GLU A 64 REMARK 465 ARG A 65 REMARK 465 GLY A 102 REMARK 465 SER A 103 REMARK 465 LYS A 104 REMARK 465 ALA A 105 REMARK 465 LEU A 106 REMARK 465 GLU A 107 REMARK 465 HIS A 108 REMARK 465 HIS A 109 REMARK 465 HIS A 110 REMARK 465 HIS A 111 REMARK 465 HIS A 112 REMARK 465 HIS A 113 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 ARG A 43 8.73 59.66 REMARK 500 LEU A 94 -66.32 -127.13 REMARK 500 REMARK 500 REMARK: NULL DBREF1 6LXL A 2 105 UNP A0A376JR14_ECOLX DBREF2 6LXL A A0A376JR14 126 229 SEQADV 6LXL MET A 1 UNP A0A376JR1 INITIATING METHIONINE SEQADV 6LXL LEU A 106 UNP A0A376JR1 EXPRESSION TAG SEQADV 6LXL GLU A 107 UNP A0A376JR1 EXPRESSION TAG SEQADV 6LXL HIS A 108 UNP A0A376JR1 EXPRESSION TAG SEQADV 6LXL HIS A 109 UNP A0A376JR1 EXPRESSION TAG SEQADV 6LXL HIS A 110 UNP A0A376JR1 EXPRESSION TAG SEQADV 6LXL HIS A 111 UNP A0A376JR1 EXPRESSION TAG SEQADV 6LXL HIS A 112 UNP A0A376JR1 EXPRESSION TAG SEQADV 6LXL HIS A 113 UNP A0A376JR1 EXPRESSION TAG SEQRES 1 A 113 MET ALA VAL ILE ALA PHE GLY LYS PHE LYS LEU ASN LEU SEQRES 2 A 113 GLY THR ARG GLU MET PHE ARG GLU ASP GLU PRO MET PRO SEQRES 3 A 113 LEU THR SER GLY GLU PHE ALA VAL LEU LYS ALA LEU VAL SEQRES 4 A 113 SER HIS PRO ARG GLU PRO LEU SER ARG ASP LYS LEU MET SEQRES 5 A 113 ASN LEU ALA ARG GLY ARG GLU TYR SER ALA MET GLU ARG SEQRES 6 A 113 SER ILE ASP VAL GLN ILE SER ARG LEU ARG ARG MET VAL SEQRES 7 A 113 GLU GLU ASP PRO ALA HIS PRO ARG TYR ILE GLN THR VAL SEQRES 8 A 113 TRP GLY LEU GLY TYR VAL PHE VAL PRO ASP GLY SER LYS SEQRES 9 A 113 ALA LEU GLU HIS HIS HIS HIS HIS HIS HELIX 1 AA1 THR A 28 SER A 40 1 13 HELIX 2 AA2 SER A 47 LEU A 54 1 8 HELIX 3 AA3 ILE A 67 GLU A 79 1 13 SHEET 1 AA1 4 VAL A 3 PHE A 6 0 SHEET 2 AA1 4 PHE A 9 ASN A 12 -1 O LEU A 11 N ILE A 4 SHEET 3 AA1 4 GLU A 17 ARG A 20 -1 O GLU A 17 N ASN A 12 SHEET 4 AA1 4 PRO A 24 MET A 25 -1 O MET A 25 N MET A 18 SHEET 1 AA2 2 ILE A 88 VAL A 91 0 SHEET 2 AA2 2 GLY A 95 PHE A 98 -1 O VAL A 97 N GLN A 89 CRYST1 60.297 60.297 83.748 90.00 90.00 90.00 P 43 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 0.016585 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016585 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011941 0.00000