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 THAT IS TITLE 3 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 SEQUENCE.; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: KLUYVEROMYCES LACTIS; SOURCE 6 ORGANISM_TAXID: 28985; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PHN280R KEYWDS CRYSTAL-PACKING INTERFACE, CRYSTALLIZATION, PROTEIN-DNA INTERFACE, KEYWDS 2 PROTEIN-PROTEIN INTERFACE, STATIC DISORDER, TRANSCRIPTION-DNA KEYWDS 3 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR O.LITTLEFIELD,H.C.M.NELSON REVDAT 6 20-NOV-24 1FYK 1 REMARK REVDAT 5 03-NOV-21 1FYK 1 SEQADV SEQRES LINK 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 CRYSTALLIZATION OF A JRNL TITL 2 SITE-SPECIFIC DNA BINDING 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' HELIX-TURN-HELIX REMARK 1 TITL 2 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 : 746 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) : 1.593 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: REMARK 3 THE STRUCTURE WAS ORIGINALLY REFINED BY MISTAKE WITH METHIONINE IN REMARK 3 LIEU OF REMARK 3 SELENOMETHIONINE. THE DEPOSITED COORDINATES HAVE BEEN ADJUSTED TO REMARK 3 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. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB. REMARK 100 THE DEPOSITION ID IS D_1000012018. 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 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 DOMAIN/DNA REMARK 900 COMPLEX REMARK 900 RELATED ID: 2HTS RELATED DB: PDB REMARK 900 2HTS IS THE HEAT SHOCK TRANSCRIPTION FACTOR DNA-BINDING DOMAIN REMARK 900 RELATED ID: 1FYL RELATED DB: PDB REMARK 900 1FYL IS THE SERENDIPITOUS CRYSTAL STRUCTURE CONTAINING THE HEAT REMARK 900 SHOCK TRANSCRIPTION FACTOR'S DNA BINDING DOMAIN AND COGNATE DNA IN REMARK 900 A HEAD-TO-HEAD ORIENTATION REMARK 900 RELATED ID: 1FYM RELATED DB: PDB REMARK 900 1FYM IS THE SERENDIPITOUS CRYSTAL STRUCTURE CONTAINING THE HEAT REMARK 900 SHOCK TRANSCRIPTION FACTOR'S DNA BINDING DOMAIN AND COGNATE DNA IN REMARK 900 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 MUTATION SEQADV 1FYK HIS A 283 UNP P22121 PHE 283 ENGINEERED MUTATION SEQADV 1FYK ALA A 284 UNP P22121 LYS 284 ENGINEERED MUTATION 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