HEADER TRANSCRIPTION/DNA 02-OCT-00 1FYK TITLE SERENDIPITOUS CRYSTAL STRUCTURE CONTAINING THE HEAT SHOCK TITLE 2 TRANSCRIPTION FACTOR'S DNA BINDING DOMAIN AND COGNATE DNA TITLE 3 THAT IS TRANSLATIONALLY DISORDERED COMPND MOL_ID: 1; COMPND 2 MOLECULE: HSE DNA-PHOSPHATE BACKBONE; COMPND 3 CHAIN: C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HEAT SHOCK FACTOR PROTEIN; COMPND 7 CHAIN: A; COMPND 8 FRAGMENT: DNA BINDING DOMAIN; COMPND 9 SYNONYM: HEAT SHOCK TRANSCRIPTION FACTOR; COMPND 10 ENGINEERED: YES; COMPND 11 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE IS BASED ON AN IDEALIZED HSE SOURCE 4 SEQUENCE.; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: KLUYVEROMYCES LACTIS; SOURCE 7 ORGANISM_TAXID: 28985; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PHN280R KEYWDS CRYSTAL-PACKING INTERFACE, CRYSTALLIZATION, PROTEIN-DNA KEYWDS 2 INTERFACE, PROTEIN-PROTEIN INTERFACE, STATIC DISORDER, KEYWDS 3 TRANSCRIPTION/DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR O.LITTLEFIELD,H.C.M.NELSON REVDAT 4 24-FEB-09 1FYK 1 VERSN REVDAT 3 08-AUG-06 1FYK 1 REMARK REVDAT 2 01-APR-03 1FYK 1 JRNL REVDAT 1 28-SEP-01 1FYK 0 JRNL AUTH O.LITTLEFIELD,H.C.NELSON JRNL TITL CRYSTAL PACKING INTERACTION THAT BLOCKS JRNL TITL 2 CRYSTALLIZATION OF A SITE-SPECIFIC DNA BINDING JRNL TITL 3 PROTEIN-DNA COMPLEX. JRNL REF PROTEINS V. 45 219 2001 JRNL REFN ISSN 0887-3585 JRNL PMID 11599025 JRNL DOI 10.1002/PROT.1142 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH O.LITTLEFIELD,H.C.M.NELSON REMARK 1 TITL A NEW USE FOR THE 'WING' OF THE 'WINGED' REMARK 1 TITL 2 HELIX-TURN-HELIX MOTIF IN THE HSF-DNA COCRYSTAL REMARK 1 REF NAT.STRUCT.BIOL. V. 6 464 1999 REMARK 1 REFN ISSN 1072-8368 REMARK 1 DOI 10.1038/8269 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 4939 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 518 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 778 REMARK 3 NUCLEIC ACID ATOMS : 41 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 38 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.59 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE WAS ORIGINALLY REFINED REMARK 3 BY MISTAKE WITH METHIONINE IN LIEU OF SELENOMETHIONINE. THE REMARK 3 DEPOSITED COORDINATES HAVE BEEN ADJUSTED TO CONTAIN REMARK 3 SELENOMETHIONINE. BECAUSE THE REFINEMENT USED GROUP B-FACTORS, REMARK 3 THE B-FACTORS WERE KEPT THE SAME. REMARK 4 REMARK 4 1FYK COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB ON 10-OCT-00. REMARK 100 THE RCSB ID CODE IS RCSB012018. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-95 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL1-5 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99981 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : FUJI REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4940 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.11300 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: NULL REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, CACODYLATE, AMMONIUM REMARK 280 ACETATE, PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 291K 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 51.57500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.49500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 51.57500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 16.49500 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 300 REMARK: PROTEIN AND DNA ARE NOT INTERACTING IN A PHYSIOLOGICALLY REMARK 300 RELEVANT MANNER 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 APPLY THE FOLLOWING TO CHAINS: C, 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 0.00000 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 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 267 REMARK 465 MSE A 268 REMARK 465 LEU A 269 REMARK 465 SER A 270 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 THR A 218 104.46 -40.86 REMARK 500 GLN A 261 75.31 -117.77 REMARK 500 SER A 265 77.54 -67.66 REMARK 500 ASN A 272 -145.66 -81.71 REMARK 500 ASP A 273 -3.85 -44.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3HTS RELATED DB: PDB REMARK 900 3HTS IS THE HEAT SHOCK TRANSCRIPTION FACTOR DNA-BINDING REMARK 900 DOMAIN/DNA COMPLEX REMARK 900 RELATED ID: 2HTS RELATED DB: PDB REMARK 900 2HTS IS THE HEAT SHOCK TRANSCRIPTION FACTOR DNA-BINDING REMARK 900 DOMAIN REMARK 900 RELATED ID: 1FYL RELATED DB: PDB REMARK 900 1FYL IS THE SERENDIPITOUS CRYSTAL STRUCTURE CONTAINING THE REMARK 900 HEAT SHOCK TRANSCRIPTION FACTOR'S DNA BINDING DOMAIN AND REMARK 900 COGNATE DNA IN A HEAD-TO-HEAD ORIENTATION REMARK 900 RELATED ID: 1FYM RELATED DB: PDB REMARK 900 1FYM IS THE SERENDIPITOUS CRYSTAL STRUCTURE CONTAINING THE REMARK 900 HEAT SHOCK TRANSCRIPTION FACTOR'S DNA BINDING DOMAIN AND REMARK 900 COGNATE DNA IN A TAIL-TO-TAIL ORIENTATION DBREF 1FYK A 193 284 UNP P22121 HSF_KLULA 193 284 DBREF 1FYK C 1 4 PDB 1FYK 1FYK 1 4 SEQADV 1FYK MSE A 204 UNP P22121 MET 204 MODIFIED RESIDUE SEQADV 1FYK MSE A 254 UNP P22121 MET 254 MODIFIED RESIDUE SEQADV 1FYK MSE A 268 UNP P22121 MET 268 MODIFIED RESIDUE SEQADV 1FYK ARG A 282 UNP P22121 ASN 282 ENGINEERED SEQADV 1FYK HIS A 283 UNP P22121 PHE 283 ENGINEERED SEQADV 1FYK ALA A 284 UNP P22121 LYS 284 ENGINEERED SEQRES 1 C 4 N N N N SEQRES 1 A 92 ALA ARG PRO ALA PHE VAL ASN LYS LEU TRP SER MSE VAL SEQRES 2 A 92 ASN ASP LYS SER ASN GLU LYS PHE ILE HIS TRP SER THR SEQRES 3 A 92 SER GLY GLU SER ILE VAL VAL PRO ASN ARG GLU ARG PHE SEQRES 4 A 92 VAL GLN GLU VAL LEU PRO LYS TYR PHE LYS HIS SER ASN SEQRES 5 A 92 PHE ALA SER PHE VAL ARG GLN LEU ASN MSE TYR GLY TRP SEQRES 6 A 92 HIS LYS VAL GLN ASP VAL LYS SER GLY SER MSE LEU SER SEQRES 7 A 92 ASN ASN ASP SER ARG TRP GLU PHE GLU ASN GLU ARG HIS SEQRES 8 A 92 ALA MODRES 1FYK MSE A 204 MET SELENOMETHIONINE MODRES 1FYK MSE A 254 MET SELENOMETHIONINE HET MSE A 204 8 HET MSE A 254 8 HETNAM MSE SELENOMETHIONINE FORMUL 2 MSE 2(C5 H11 N O2 SE) FORMUL 3 HOH *38(H2 O) HELIX 1 1 PRO A 195 ASP A 207 1 13 HELIX 2 2 LYS A 208 GLU A 211 5 4 HELIX 3 3 ASN A 227 VAL A 235 1 9 HELIX 4 4 LEU A 236 TYR A 239 5 4 HELIX 5 5 ASN A 244 TYR A 255 1 12 SHEET 1 A 4 HIS A 215 TRP A 216 0 SHEET 2 A 4 ILE A 223 VAL A 225 -1 N VAL A 224 O HIS A 215 SHEET 3 A 4 TRP A 276 ASN A 280 -1 O TRP A 276 N VAL A 225 SHEET 4 A 4 TRP A 257 LYS A 259 -1 N HIS A 258 O GLU A 279 LINK C SER A 203 N MSE A 204 1555 1555 1.33 LINK C MSE A 204 N VAL A 205 1555 1555 1.33 LINK C ASN A 253 N MSE A 254 1555 1555 1.33 LINK C MSE A 254 N TYR A 255 1555 1555 1.33 CRYST1 103.150 32.990 42.570 90.00 109.90 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 0.009695 0.000000 0.003509 0.00000 SCALE2 0.000000 0.030312 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024982 0.00000 MASTER 266 0 2 5 4 0 0 6 0 0 0 9 END