HEADER TRANSCRIPTION 06-MAR-24 8YLF TITLE CRYSTAL STRUCTURE OF BURKHOLDERIA THAILANDENSIS MFTR COMPND MOL_ID: 1; COMPND 2 MOLECULE: MARR FAMILY TRANSCRIPTIONAL REGULATOR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BURKHOLDERIA THAILANDENSIS; SOURCE 3 ORGANISM_TAXID: 57975; SOURCE 4 GENE: A8H32_16025; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS TRANSCRIPTION FACTOR, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR W.S.SONG,S.I.YOON REVDAT 1 13-NOV-24 8YLF 0 JRNL AUTH W.S.SONG,D.U.KI,H.Y.CHO,O.H.KWON,H.CHO,S.I.YOON JRNL TITL STRUCTURAL BASIS OF TRANSCRIPTIONAL REGULATION BY URTR IN JRNL TITL 2 RESPONSE TO URIC ACID. JRNL REF NUCLEIC ACIDS RES. 2024 JRNL REFN ESSN 1362-4962 JRNL PMID 39484741 JRNL DOI 10.1093/NAR/GKAE922 REMARK 2 REMARK 2 RESOLUTION. 2.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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) : 2.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 11952 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.860 REMARK 3 FREE R VALUE TEST SET COUNT : 581 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 28.9300 - 3.1900 1.00 2954 146 0.1996 0.2019 REMARK 3 2 3.1900 - 2.5300 1.00 2855 131 0.2494 0.2787 REMARK 3 3 2.5300 - 2.2100 1.00 2802 139 0.2213 0.2772 REMARK 3 4 2.2100 - 2.0100 1.00 2760 165 0.2373 0.3019 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) : 0.182 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.003 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.12 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 : 0.006 1163 REMARK 3 ANGLE : 0.796 1579 REMARK 3 CHIRALITY : 0.045 187 REMARK 3 PLANARITY : 0.005 207 REMARK 3 DIHEDRAL : 10.303 715 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 78 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.8535 16.4304 11.1413 REMARK 3 T TENSOR REMARK 3 T11: 0.2881 T22: 0.1554 REMARK 3 T33: 0.2450 T12: 0.0262 REMARK 3 T13: 0.0141 T23: 0.0043 REMARK 3 L TENSOR REMARK 3 L11: 8.1781 L22: 1.3281 REMARK 3 L33: 2.0036 L12: 2.4664 REMARK 3 L13: 1.4662 L23: 0.6212 REMARK 3 S TENSOR REMARK 3 S11: -0.1824 S12: 0.0162 S13: -0.1052 REMARK 3 S21: -0.1023 S22: 0.0751 S23: -0.1130 REMARK 3 S31: 0.0878 S32: 0.0252 S33: 0.0520 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 79 THROUGH 160 ) REMARK 3 ORIGIN FOR THE GROUP (A): -22.0862 11.9098 7.9972 REMARK 3 T TENSOR REMARK 3 T11: 0.3116 T22: 0.2477 REMARK 3 T33: 0.2158 T12: -0.0234 REMARK 3 T13: 0.0022 T23: -0.0370 REMARK 3 L TENSOR REMARK 3 L11: 5.6725 L22: 1.4284 REMARK 3 L33: 3.3695 L12: 0.4122 REMARK 3 L13: 2.2659 L23: -0.5732 REMARK 3 S TENSOR REMARK 3 S11: -0.0922 S12: -0.0453 S13: -0.2444 REMARK 3 S21: -0.0943 S22: 0.0340 S23: -0.0521 REMARK 3 S31: 0.0117 S32: -0.4057 S33: 0.0620 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 8YLF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-MAR-24. REMARK 100 THE DEPOSITION ID IS D_1300045757. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-NOV-19 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 : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11986 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.010 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 10.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 53.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.04 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.20 REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: IN-HOUSE SE-SAD MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: IMIDAZOLE, SODIUM CITRATE, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-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 25.75133 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 51.50267 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 51.50267 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 25.75133 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: 6880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 25.75133 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 SER A -4 REMARK 465 ALA A -3 REMARK 465 LYS A -2 REMARK 465 ASP A -1 REMARK 465 PRO A 0 REMARK 465 ASN A 104 REMARK 465 PRO A 105 REMARK 465 ALA A 106 REMARK 465 ASP A 107 REMARK 465 GLY A 108 REMARK 465 ARG A 109 REMARK 465 GLY A 110 REMARK 465 ALA A 161 REMARK 465 ALA A 162 REMARK 465 GLU A 163 REMARK 465 GLY A 164 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 LYS A 95 CD CE NZ REMARK 470 ARG A 102 CG CD NE CZ NH1 NH2 REMARK 470 THR A 111 OG1 CG2 REMARK 470 ARG A 135 CD NE CZ NH1 NH2 REMARK 470 ARG A 136 NE CZ NH1 NH2 REMARK 470 ARG A 147 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 151 CG CD CE NZ REMARK 470 GLN A 158 CD OE1 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 ARG A 40 -56.08 -124.08 REMARK 500 SER A 82 51.01 -92.20 REMARK 500 REMARK 500 REMARK: NULL DBREF1 8YLF A 1 164 UNP A0A2N8QSC4_BURTH DBREF2 8YLF A A0A2N8QSC4 1 164 SEQADV 8YLF SER A -4 UNP A0A2N8QSC EXPRESSION TAG SEQADV 8YLF ALA A -3 UNP A0A2N8QSC EXPRESSION TAG SEQADV 8YLF LYS A -2 UNP A0A2N8QSC EXPRESSION TAG SEQADV 8YLF ASP A -1 UNP A0A2N8QSC EXPRESSION TAG SEQADV 8YLF PRO A 0 UNP A0A2N8QSC EXPRESSION TAG SEQRES 1 A 169 SER ALA LYS ASP PRO MET ASP ARG ALA ALA HIS ALA VAL SEQRES 2 A 169 GLU GLN TRP ARG SER GLU ARG PRO ASP LEU ASP PRO SER SEQRES 3 A 169 SER MET ILE VAL LEU GLY ARG LEU GLN GLU ALA ALA LEU SEQRES 4 A 169 VAL ILE ALA ARG ASP ARG LEU ASN PRO LEU PHE ALA ARG SEQRES 5 A 169 TYR GLY LEU GLN PRO GLY GLU PHE ASP VAL LEU ALA THR SEQRES 6 A 169 LEU ARG ARG SER GLY ALA PRO TYR ALA LEU THR PRO THR SEQRES 7 A 169 ALA LEU TYR ASP ALA ALA MET ILE SER SER GLY SER MET SEQRES 8 A 169 THR ASN ARG ILE ASP ARG LEU GLU LYS ALA GLY TRP VAL SEQRES 9 A 169 GLU ARG ARG ALA ASN PRO ALA ASP GLY ARG GLY THR LEU SEQRES 10 A 169 VAL ALA LEU THR SER ALA GLY ARG ALA LEU ILE ASP ASP SEQRES 11 A 169 ALA VAL VAL ALA HIS VAL ASP ASN GLN ARG ARG VAL LEU SEQRES 12 A 169 SER ALA LEU SER ALA ALA GLU GLN ARG GLN LEU ALA LYS SEQRES 13 A 169 LEU LEU ASP LYS LEU LEU GLN GLY GLN ALA ALA GLU GLY FORMUL 2 HOH *16(H2 O) HELIX 1 AA1 ASP A 2 ARG A 15 1 14 HELIX 2 AA2 SER A 22 ARG A 40 1 19 HELIX 3 AA3 ARG A 40 TYR A 48 1 9 HELIX 4 AA4 GLN A 51 SER A 64 1 14 HELIX 5 AA5 THR A 71 ALA A 79 1 9 HELIX 6 AA6 SER A 85 ALA A 96 1 12 HELIX 7 AA7 THR A 116 SER A 139 1 24 HELIX 8 AA8 SER A 142 GLY A 159 1 18 SHEET 1 AA1 3 ALA A 69 LEU A 70 0 SHEET 2 AA1 3 LEU A 112 LEU A 115 -1 O VAL A 113 N LEU A 70 SHEET 3 AA1 3 VAL A 99 ARG A 102 -1 N ARG A 102 O LEU A 112 CISPEP 1 ALA A 66 PRO A 67 0 2.12 CRYST1 62.389 62.389 77.254 90.00 90.00 120.00 P 31 2 1 6 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 0.016028 0.009254 0.000000 0.00000 SCALE2 0.000000 0.018508 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012944 0.00000