HEADER TRANSCRIPTION 06-APR-24 8YZ7 TITLE CRYSTAL STRUCTURE OF DDRI, A CRP FAMILY PROTEIN FROM DEINOCOCCUS TITLE 2 RADIODURANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REGULATOR, FNR/CRP FAMILY; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: THE GENBANK ACCESSION NUMBER A2G07_08515 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DEINOCOCCUS RADIODURANS R1 = ATCC 13939 = DSM SOURCE 3 20539; SOURCE 4 ORGANISM_TAXID: 243230; SOURCE 5 ATCC: 13939; SOURCE 6 GENE: DR_0997; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS DNA BINDING, GENE REGULATION, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR Y.ZHAO,Y.WANG REVDAT 3 11-SEP-24 8YZ7 1 JRNL REVDAT 2 31-JUL-24 8YZ7 1 JRNL REVDAT 1 03-JUL-24 8YZ7 0 JRNL AUTH Y.WANG,J.HU,X.GAO,Y.CAO,S.YE,C.CHEN,L.WANG,H.XU,M.GUO, JRNL AUTH 2 D.ZHANG,R.ZHOU,Y.HUA,Y.ZHAO JRNL TITL CAMP-INDEPENDENT DNA BINDING OF THE CRP FAMILY PROTEIN DDRI JRNL TITL 2 FROM DEINOCOCCUS RADIODURANS. JRNL REF MBIO V. 15 14424 2024 JRNL REFN ESSN 2150-7511 JRNL PMID 38916345 JRNL DOI 10.1128/MBIO.01144-24 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 18612 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.290 REMARK 3 FREE R VALUE TEST SET COUNT : 984 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 25.8900 - 3.8200 1.00 2644 134 0.1733 0.1953 REMARK 3 2 3.8200 - 3.0400 1.00 2536 129 0.2005 0.2005 REMARK 3 3 3.0300 - 2.6500 1.00 2514 145 0.2421 0.2990 REMARK 3 4 2.6500 - 2.4100 1.00 2466 175 0.2516 0.2679 REMARK 3 5 2.4100 - 2.2400 1.00 2496 122 0.2477 0.2755 REMARK 3 6 2.2400 - 2.1100 1.00 2482 136 0.2082 0.2729 REMARK 3 7 2.1100 - 2.0000 1.00 2490 143 0.2345 0.2471 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.020 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 NULL REMARK 3 ANGLE : 0.779 NULL REMARK 3 CHIRALITY : 0.047 241 REMARK 3 PLANARITY : 0.006 255 REMARK 3 DIHEDRAL : 10.656 538 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND ( RESID 301:303 OR RESID 401:465 ) ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.821 -33.502 -9.543 REMARK 3 T TENSOR REMARK 3 T11: 0.2505 T22: 0.3147 REMARK 3 T33: 0.2914 T12: 0.0063 REMARK 3 T13: -0.0114 T23: 0.0595 REMARK 3 L TENSOR REMARK 3 L11: 1.2114 L22: 1.0610 REMARK 3 L33: 1.4875 L12: -0.5616 REMARK 3 L13: -0.3249 L23: 0.8168 REMARK 3 S TENSOR REMARK 3 S11: 0.0101 S12: 0.0245 S13: 0.1485 REMARK 3 S21: -0.0502 S22: -0.0909 S23: -0.0002 REMARK 3 S31: -0.0195 S32: 0.1453 S33: 0.0000 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 8YZ7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 08-APR-24. REMARK 100 THE DEPOSITION ID IS D_1300046710. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL02U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18623 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 : 19.70 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.7700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.61300 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: 2ZCW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: BIS-TRIS, KCL, PH 6.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 41.09333 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 20.54667 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 20.54667 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 41.09333 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: 3980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 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 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 THR A 2 REMARK 465 GLN A 3 REMARK 465 THR A 4 REMARK 465 GLN A 5 REMARK 465 THR A 6 REMARK 465 ALA A 7 REMARK 465 ALA A 8 REMARK 465 ARG A 9 REMARK 465 THR A 10 REMARK 465 PHE A 11 REMARK 465 ALA A 203 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 30 -88.34 -147.86 REMARK 500 REMARK 500 REMARK: NULL DBREF 8YZ7 A 1 203 PDB 8YZ7 8YZ7 1 203 SEQRES 1 A 203 MET THR GLN THR GLN THR ALA ALA ARG THR PHE VAL ASP SEQRES 2 A 203 THR VAL THR TYR ARG PRO GLY ALA VAL ILE LEU TYR PRO SEQRES 3 A 203 GLY LYS SER ASP MET LEU TYR ARG VAL SER SER GLY LEU SEQRES 4 A 203 VAL ARG VAL HIS THR MET ASP ASP ASP GLY ASN GLY LEU SEQRES 5 A 203 THR LEU ARG TYR VAL LYS PRO GLY GLU TYR PHE GLY GLU SEQRES 6 A 203 GLU ALA LEU ALA GLY VAL ASN ARG ALA TYR PHE ALA GLU SEQRES 7 A 203 ALA VAL THR ASP SER ALA ILE ASP VAL ILE ASN PRO ALA SEQRES 8 A 203 LEU MET SER ALA GLU ASP ASN LEU VAL VAL THR THR HIS SEQRES 9 A 203 LEU VAL ARG THR LEU GLU ARG ALA TYR GLU SER ILE TYR SEQRES 10 A 203 ARG LEU VAL GLY LYS ARG LEU ARG ALA ARG ILE ALA GLY SEQRES 11 A 203 GLU LEU LEU GLU LEU LYS ASP THR ALA LEU ALA THR GLN SEQRES 12 A 203 LEU ASP SER GLY GLU THR MET ILE TYR ALA THR HIS ASP SEQRES 13 A 203 GLU LEU ALA ALA ALA VAL GLY SER VAL ARG GLU THR VAL SEQRES 14 A 203 THR LYS VAL VAL GLY GLU LEU SER ARG GLU GLY VAL ILE SEQRES 15 A 203 SER ALA GLY TYR GLY LYS ILE THR LEU LYS ASP GLU ARG SEQRES 16 A 203 ALA LEU ALA THR ILE ALA ALA ALA HET K A 301 1 HET K A 302 1 HET K A 303 1 HETNAM K POTASSIUM ION FORMUL 2 K 3(K 1+) FORMUL 5 HOH *65(H2 O) HELIX 1 AA1 GLU A 65 GLY A 70 1 6 HELIX 2 AA2 SER A 94 LYS A 122 1 29 HELIX 3 AA3 ARG A 123 LYS A 136 1 14 HELIX 4 AA4 THR A 154 GLY A 163 1 10 HELIX 5 AA5 VAL A 165 GLU A 179 1 15 HELIX 6 AA6 ASP A 193 ALA A 202 1 10 SHEET 1 AA1 4 ASP A 13 TYR A 17 0 SHEET 2 AA1 4 SER A 83 ILE A 88 -1 O VAL A 87 N ASP A 13 SHEET 3 AA1 4 LEU A 32 SER A 37 -1 N LEU A 32 O ILE A 88 SHEET 4 AA1 4 TYR A 62 PHE A 63 -1 O PHE A 63 N TYR A 33 SHEET 1 AA2 4 VAL A 22 LEU A 24 0 SHEET 2 AA2 4 PHE A 76 ALA A 79 -1 O ALA A 77 N ILE A 23 SHEET 3 AA2 4 VAL A 40 MET A 45 -1 N HIS A 43 O PHE A 76 SHEET 4 AA2 4 GLY A 51 VAL A 57 -1 O LEU A 54 N VAL A 42 SHEET 1 AA3 4 ALA A 141 GLN A 143 0 SHEET 2 AA3 4 THR A 149 TYR A 152 -1 O MET A 150 N THR A 142 SHEET 3 AA3 4 LYS A 188 LEU A 191 -1 O LEU A 191 N THR A 149 SHEET 4 AA3 4 ILE A 182 ALA A 184 -1 N SER A 183 O THR A 190 LINK K K A 301 O HOH A 445 1555 1555 3.37 LINK K K A 303 O HOH A 404 1555 1555 3.06 CRYST1 87.170 87.170 61.640 90.00 90.00 120.00 P 32 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 0.011472 0.006623 0.000000 0.00000 SCALE2 0.000000 0.013247 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016223 0.00000