HEADER TRANSCRIPTION 06-MAR-24 8YLJ TITLE CRYSTAL STRUCTURE OF PECTOBACTERIUM ATROSEPTICUM PECS IN COMPLEX WITH TITLE 2 URIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: REGULATORY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PECTOBACTERIUM ATROSEPTICUM; SOURCE 3 ORGANISM_TAXID: 29471; SOURCE 4 GENE: PECS, ECA2036; 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 8YLJ 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. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 10862 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 539 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 26.2600 - 3.2500 0.99 2710 123 0.2030 0.2488 REMARK 3 2 3.2500 - 2.5800 1.00 2563 146 0.2456 0.2898 REMARK 3 3 2.5800 - 2.2600 1.00 2516 154 0.2529 0.3084 REMARK 3 4 2.2600 - 2.0500 1.00 2534 116 0.2692 0.2853 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) : 0.198 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.971 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.96 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.71 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 : 0.002 1266 REMARK 3 ANGLE : 0.431 1719 REMARK 3 CHIRALITY : 0.033 204 REMARK 3 PLANARITY : 0.004 222 REMARK 3 DIHEDRAL : 12.051 461 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 14 THROUGH 60 ) REMARK 3 ORIGIN FOR THE GROUP (A): -35.1746 -2.5600 -6.9565 REMARK 3 T TENSOR REMARK 3 T11: 0.1547 T22: 0.2057 REMARK 3 T33: 0.1625 T12: 0.0596 REMARK 3 T13: 0.0353 T23: 0.0116 REMARK 3 L TENSOR REMARK 3 L11: 5.5386 L22: 2.7660 REMARK 3 L33: 2.3335 L12: -0.2853 REMARK 3 L13: 0.5723 L23: -0.6912 REMARK 3 S TENSOR REMARK 3 S11: -0.0296 S12: 0.1156 S13: 0.0688 REMARK 3 S21: 0.2228 S22: -0.0216 S23: 0.0180 REMARK 3 S31: -0.0524 S32: -0.2296 S33: -0.1072 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 61 THROUGH 128 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.5260 7.5994 -20.8786 REMARK 3 T TENSOR REMARK 3 T11: 0.3303 T22: 0.5908 REMARK 3 T33: 0.3164 T12: -0.0822 REMARK 3 T13: -0.0184 T23: 0.1993 REMARK 3 L TENSOR REMARK 3 L11: 2.2147 L22: 2.8702 REMARK 3 L33: 2.4196 L12: -0.5223 REMARK 3 L13: 0.1099 L23: -1.1581 REMARK 3 S TENSOR REMARK 3 S11: -0.0510 S12: 1.2029 S13: 0.5135 REMARK 3 S21: -0.4669 S22: 0.2369 S23: 0.0993 REMARK 3 S31: 0.0574 S32: -0.1292 S33: -0.0618 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 129 THROUGH 175 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.1956 9.3132 -4.0542 REMARK 3 T TENSOR REMARK 3 T11: 0.2847 T22: 0.2035 REMARK 3 T33: 0.3844 T12: 0.0091 REMARK 3 T13: 0.0105 T23: 0.0255 REMARK 3 L TENSOR REMARK 3 L11: 4.9053 L22: 3.4347 REMARK 3 L33: 2.0223 L12: 2.5432 REMARK 3 L13: -0.6469 L23: -0.9348 REMARK 3 S TENSOR REMARK 3 S11: 0.1341 S12: -0.2326 S13: 1.0183 REMARK 3 S21: 0.0840 S22: -0.2561 S23: 0.0692 REMARK 3 S31: -0.2705 S32: 0.0244 S33: 0.0047 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 8YLJ 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_1300045756. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-22 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 : 10908 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 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: 8YLF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6000, HEPES, LITHIUM CHLORIDE, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 26.26400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.39800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.26400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.39800 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 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 -1.000000 0.000000 0.000000 -52.52800 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 323 LIES ON A SPECIAL POSITION. 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 10 REMARK 465 ALA A 11 REMARK 465 LYS A 12 REMARK 465 ASP A 13 REMARK 465 ASN A 176 REMARK 465 LYS A 177 REMARK 465 GLY A 178 REMARK 465 ASN A 179 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 14 CG CD1 CD2 REMARK 470 ARG A 25 NE CZ NH1 NH2 REMARK 470 SER A 55 OG REMARK 470 SER A 95 OG REMARK 470 LYS A 103 CG CD CE NZ REMARK 470 GLU A 112 CG CD OE1 OE2 REMARK 470 ARG A 113 CZ NH1 NH2 REMARK 470 GLU A 117 CG CD OE1 OE2 REMARK 470 SER A 122 OG REMARK 470 THR A 123 OG1 CG2 REMARK 470 SER A 130 OG REMARK 470 GLU A 133 CD OE1 OE2 REMARK 470 GLU A 144 CG CD OE1 OE2 REMARK 470 GLU A 156 CG CD OE1 OE2 REMARK 470 SER A 174 OG 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 ASP A 15 -169.72 -123.76 REMARK 500 SER A 95 -153.73 -157.36 REMARK 500 REMARK 500 REMARK: NULL DBREF 8YLJ A 15 179 UNP Q6D5K4 Q6D5K4_PECAS 15 179 SEQADV 8YLJ SER A 10 UNP Q6D5K4 EXPRESSION TAG SEQADV 8YLJ ALA A 11 UNP Q6D5K4 EXPRESSION TAG SEQADV 8YLJ LYS A 12 UNP Q6D5K4 EXPRESSION TAG SEQADV 8YLJ ASP A 13 UNP Q6D5K4 EXPRESSION TAG SEQADV 8YLJ LEU A 14 UNP Q6D5K4 EXPRESSION TAG SEQRES 1 A 170 SER ALA LYS ASP LEU ASP ALA VAL ASP ALA ILE LEU GLU SEQRES 2 A 170 GLN TRP ARG ARG GLU ARG PRO ASP LEU ASP ALA SER PRO SEQRES 3 A 170 MET GLY PRO ILE GLY ARG LEU ARG ARG CYS ALA VAL LEU SEQRES 4 A 170 MET ASP GLN ARG LEU GLU SER CYS PHE SER ARG PHE ASP SEQRES 5 A 170 LEU SER SER TRP GLU PHE ASP MET LEU ALA THR LEU ARG SEQRES 6 A 170 ARG ALA GLY ALA PRO HIS CYS LEU SER PRO THR GLU LEU SEQRES 7 A 170 PHE SER THR LEU MET VAL THR SER GLY THR MET THR HIS SEQRES 8 A 170 ARG LEU LYS ARG LEU GLU THR ARG GLY PHE ILE GLU ARG SEQRES 9 A 170 VAL GLN ASN GLU LEU ASP ALA ARG SER THR LEU VAL GLN SEQRES 10 A 170 LEU THR SER SER GLY LEU GLU LEU ILE ASN ARG ALA VAL SEQRES 11 A 170 GLU ALA HIS ILE GLU ASN GLU ARG GLN VAL LEU SER VAL SEQRES 12 A 170 LEU PRO ALA GLU VAL LEU ALA ALA LEU ASP THR ASN LEU SEQRES 13 A 170 ALA ALA LEU LEU ARG GLY LEU GLU SER HIS ASN LYS GLY SEQRES 14 A 170 ASN HET URC A 201 12 HETNAM URC URIC ACID HETSYN URC 7,9-DIHYDRO-1H-PURINE-2,6,8(3H)-TRIONE FORMUL 2 URC C5 H4 N4 O3 FORMUL 3 HOH *37(H2 O) HELIX 1 AA1 ASP A 15 ARG A 28 1 14 HELIX 2 AA2 PRO A 35 SER A 58 1 24 HELIX 3 AA3 ARG A 59 ASP A 61 5 3 HELIX 4 AA4 SER A 63 ALA A 76 1 14 HELIX 5 AA5 SER A 83 THR A 90 1 8 HELIX 6 AA6 MET A 98 ARG A 108 1 11 HELIX 7 AA7 THR A 128 SER A 151 1 24 HELIX 8 AA8 PRO A 154 SER A 174 1 21 SHEET 1 AA1 3 CYS A 81 LEU A 82 0 SHEET 2 AA1 3 THR A 123 LEU A 127 -1 O VAL A 125 N LEU A 82 SHEET 3 AA1 3 ILE A 111 GLN A 115 -1 N VAL A 114 O LEU A 124 CISPEP 1 ALA A 78 PRO A 79 0 0.41 CRYST1 52.528 78.796 39.878 90.00 90.00 90.00 P 21 21 2 4 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 0.019037 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012691 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025076 0.00000