PDB Short entry for 5D8K HEADER TRANSCRIPTION/DNA 17-AUG-15 5D8K TITLE HUMAN HSF2 DNA-BINDING DOMAIN BOUND TO 2-SITE HSE DNA AT 1.73 TITLE 2 ANGSTROMS RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*GP*TP*TP*CP*TP*AP*GP*AP*AP*CP*C)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HEAT SHOCK FACTOR PROTEIN 2; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: HSF 2,HEAT SHOCK TRANSCRIPTION FACTOR 2,HSTF 2; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 GENE: HSF2, HSTF2; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 12 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS TRANSCRIPTION FACTOR, DNA, HSF, TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.M.JAEGER,C.W.PEMBLE,D.J.THIELE REVDAT 4 06-MAR-24 5D8K 1 REMARK REVDAT 3 10-FEB-16 5D8K 1 JRNL REVDAT 2 03-FEB-16 5D8K 1 JRNL REVDAT 1 06-JAN-16 5D8K 0 JRNL AUTH A.M.JAEGER,C.W.PEMBLE,L.SISTONEN,D.J.THIELE JRNL TITL STRUCTURES OF HSF2 REVEAL MECHANISMS FOR DIFFERENTIAL JRNL TITL 2 REGULATION OF HUMAN HEAT-SHOCK FACTORS. JRNL REF NAT.STRUCT.MOL.BIOL. V. 23 147 2016 JRNL REFN ESSN 1545-9985 JRNL PMID 26727490 JRNL DOI 10.1038/NSMB.3150 REMARK 2 REMARK 2 RESOLUTION. 1.73 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1675 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) : 1.73 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 13023 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.153 REMARK 3 R VALUE (WORKING SET) : 0.148 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1313 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 21.2157 - 3.5895 0.98 1402 161 0.1146 0.1636 REMARK 3 2 3.5895 - 2.8513 0.96 1356 150 0.1414 0.1885 REMARK 3 3 2.8513 - 2.4915 0.96 1334 150 0.1681 0.1986 REMARK 3 4 2.4915 - 2.2640 0.95 1321 150 0.1573 0.2194 REMARK 3 5 2.2640 - 2.1018 0.94 1309 142 0.1696 0.2456 REMARK 3 6 2.1018 - 1.9780 0.93 1270 146 0.1722 0.2306 REMARK 3 7 1.9780 - 1.8790 0.93 1267 139 0.1970 0.2579 REMARK 3 8 1.8790 - 1.7973 0.92 1271 138 0.2140 0.2849 REMARK 3 9 1.7973 - 1.7281 0.86 1180 137 0.2407 0.2778 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.430 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 : 0.011 1241 REMARK 3 ANGLE : 1.396 1728 REMARK 3 CHIRALITY : 0.058 181 REMARK 3 PLANARITY : 0.008 184 REMARK 3 DIHEDRAL : 20.573 485 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 5D8K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000212825. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-AUG-14 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 9 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13023 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.728 REMARK 200 RESOLUTION RANGE LOW (A) : 21.210 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.73 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 7 MG/ML PROTEIN:DNA COMPLEXES WERE REMARK 280 MIXED AT A RATIO OF 1:1.2 PROTEIN:DNA IN 25 MM HEPES PH 7.5 AND REMARK 280 150 MM NACL AND CRYSTALLIZED AGAINST 100 MM NACL, 100 MM BICINE REMARK 280 PH 9, AND 30% PEG 550 MME. CRYSTALS GREW OVERNIGHT AT ROOM REMARK 280 TEMPERATURE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 42.44150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.81550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 42.44150 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.81550 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 -0.98308 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 39.38073 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 130 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 B 112 REMARK 465 SER B 113 REMARK 465 SER B 114 REMARK 465 LYS B 115 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HG SER B 35 OE2 GLU B 90 1.52 REMARK 500 O HOH B 203 O HOH B 265 2.05 REMARK 500 REMARK 500 REMARK: NULL 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 LYS B 54 40.71 -100.77 REMARK 500 LYS B 54 40.95 -100.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5D8L RELATED DB: PDB DBREF 5D8K A 1 12 PDB 5D8K 5D8K 1 12 DBREF 5D8K B 8 115 UNP Q03933 HSF2_HUMAN 8 115 SEQADV 5D8K HIS B 6 UNP Q03933 EXPRESSION TAG SEQADV 5D8K MET B 7 UNP Q03933 EXPRESSION TAG SEQRES 1 A 12 DG DG DT DT DC DT DA DG DA DA DC DC SEQRES 1 B 110 HIS MET PRO ALA PHE LEU SER LYS LEU TRP THR LEU VAL SEQRES 2 B 110 GLU GLU THR HIS THR ASN GLU PHE ILE THR TRP SER GLN SEQRES 3 B 110 ASN GLY GLN SER PHE LEU VAL LEU ASP GLU GLN ARG PHE SEQRES 4 B 110 ALA LYS GLU ILE LEU PRO LYS TYR PHE LYS HIS ASN ASN SEQRES 5 B 110 MET ALA SER PHE VAL ARG GLN LEU ASN MET TYR GLY PHE SEQRES 6 B 110 ARG LYS VAL VAL HIS ILE ASP SER GLY ILE VAL LYS GLN SEQRES 7 B 110 GLU ARG ASP GLY PRO VAL GLU PHE GLN HIS PRO TYR PHE SEQRES 8 B 110 LYS GLN GLY GLN ASP ASP LEU LEU GLU ASN ILE LYS ARG SEQRES 9 B 110 LYS VAL SER SER SER LYS FORMUL 3 HOH *106(H2 O) HELIX 1 AA1 PRO B 8 GLU B 20 1 13 HELIX 2 AA2 THR B 21 ASN B 24 5 4 HELIX 3 AA3 ASP B 40 ILE B 48 1 9 HELIX 4 AA4 ILE B 48 PHE B 53 1 6 HELIX 5 AA5 ASN B 57 TYR B 68 1 12 HELIX 6 AA6 GLN B 100 ILE B 107 5 8 SHEET 1 AA1 4 ILE B 27 TRP B 29 0 SHEET 2 AA1 4 PHE B 36 VAL B 38 -1 O LEU B 37 N THR B 28 SHEET 3 AA1 4 VAL B 89 GLN B 92 -1 O VAL B 89 N VAL B 38 SHEET 4 AA1 4 ARG B 71 LYS B 72 -1 N ARG B 71 O GLN B 92 CRYST1 84.883 39.631 39.393 90.00 91.43 90.00 C 1 2 1 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 0.011781 0.000000 0.000295 0.00000 SCALE2 0.000000 0.025233 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025393 0.00000