PDB Short entry for 1BH9 HEADER TRANSCRIPTION REGULATION COMPLEX 16-JUN-98 1BH9 TITLE HTAFII18/HTAFII28 HETERODIMER CRYSTAL STRUCTURE WITH BOUND PCMBS COMPND MOL_ID: 1; COMPND 2 MOLECULE: TAFII18; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 31 - 75; COMPND 5 SYNONYM: TRANSCRIPTION INITIATION FACTOR TFIID 18 KD SUBUNIT; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: TAFII28; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: RESIDUES 113 - 201; COMPND 11 SYNONYM: TRANSCRIPTION INITIATION FACTOR TFIID 28 KD SUBUNIT; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELL: HELA; SOURCE 6 CELLULAR_LOCATION: NUCLEUS; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 CELL: HELA; SOURCE 16 CELLULAR_LOCATION: NUCLEUS; SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 18 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 19 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS HTAFII18, HISTONE FOLD, TATA BINDING PROTEIN, TRANSCRIPTION KEYWDS 2 REGULATION COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.BIRCK,O.POCH,C.ROMIER,M.RUFF,G.MENGUS,A.-C.LAVIGNE,I.DAVIDSON, AUTHOR 2 D.MORAS REVDAT 4 11-APR-18 1BH9 1 REMARK REVDAT 3 04-APR-18 1BH9 1 REMARK REVDAT 2 24-FEB-09 1BH9 1 VERSN REVDAT 1 22-JUN-99 1BH9 0 JRNL AUTH C.BIRCK,O.POCH,C.ROMIER,M.RUFF,G.MENGUS,A.C.LAVIGNE, JRNL AUTH 2 I.DAVIDSON,D.MORAS JRNL TITL HUMAN TAF(II)28 AND TAF(II)18 INTERACT THROUGH A HISTONE JRNL TITL 2 FOLD ENCODED BY ATYPICAL EVOLUTIONARY CONSERVED MOTIFS ALSO JRNL TITL 3 FOUND IN THE SPT3 FAMILY. JRNL REF CELL(CAMBRIDGE,MASS.) V. 94 239 1998 JRNL REFN ISSN 0092-8674 JRNL PMID 9695952 JRNL DOI 10.1016/S0092-8674(00)81423-3 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 4890 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 508 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 : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.80 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 438 REMARK 3 BIN R VALUE (WORKING SET) : 0.2850 REMARK 3 BIN FREE R VALUE : 0.3580 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 45 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 : 1074 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 64 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 50.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.90 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) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.480 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.120 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.890 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.790 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.790 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : PMB.PAR REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : PMB.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1BH9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171755. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : JAN-98 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.003 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5119 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 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 (%) : 99.3 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.17300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 15.30 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 22.90000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.05000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.20000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.05000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.90000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.20000 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: 3440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 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 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 PHE A 32 66.81 -161.49 REMARK 500 ALA B 128 143.36 -176.30 REMARK 500 SER B 140 21.67 -73.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 PMB B 300 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 173 SG REMARK 620 2 PMB B 300 C4 177.3 REMARK 620 3 GLU B 178 O 87.3 92.9 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: MRY REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: BINDING SITE OF MERCURY FROM PCMBS. REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PMB B 300 DBREF 1BH9 A 31 75 UNP Q15543 TAF13_HUMAN 31 75 DBREF 1BH9 B 113 201 UNP Q15544 TAF11_HUMAN 113 201 SEQRES 1 A 45 LEU PHE SER LYS GLU LEU ARG CYS MET MET TYR GLY PHE SEQRES 2 A 45 GLY ASP ASP GLN ASN PRO TYR THR GLU SER VAL ASP ILE SEQRES 3 A 45 LEU GLU ASP LEU VAL ILE GLU PHE ILE THR GLU MET THR SEQRES 4 A 45 HIS LYS ALA MET SER ILE SEQRES 1 B 89 PHE SER GLU GLU GLN LEU ASN ARG TYR GLU MET TYR ARG SEQRES 2 B 89 ARG SER ALA PHE PRO LYS ALA ALA ILE LYS ARG LEU ILE SEQRES 3 B 89 GLN SER ILE THR GLY THR SER VAL SER GLN ASN VAL VAL SEQRES 4 B 89 ILE ALA MET SER GLY ILE SER LYS VAL PHE VAL GLY GLU SEQRES 5 B 89 VAL VAL GLU GLU ALA LEU ASP VAL CYS GLU LYS TRP GLY SEQRES 6 B 89 GLU MET PRO PRO LEU GLN PRO LYS HIS MET ARG GLU ALA SEQRES 7 B 89 VAL ARG ARG LEU LYS SER LYS GLY GLN ILE PRO HET PMB B 300 11 HETNAM PMB PARA-MERCURY-BENZENESULFONIC ACID FORMUL 3 PMB C6 H5 HG O3 S FORMUL 4 HOH *64(H2 O) HELIX 1 1 SER A 33 GLY A 42 1 10 HELIX 2 2 THR A 51 MET A 73 1 23 HELIX 3 3 GLU B 115 ARG B 126 1 12 HELIX 4 4 LYS B 131 THR B 142 1 12 HELIX 5 5 GLN B 148 LYS B 175 1 28 HELIX 6 6 PRO B 184 SER B 196 1 13 LINK HG PMB B 300 SG CYS B 173 1555 1555 2.66 LINK HG PMB B 300 O GLU B 178 1555 1555 3.09 CISPEP 1 PRO B 180 PRO B 181 0 -0.42 SITE 1 MRY 1 CYS B 173 SITE 1 AC1 8 ALA B 132 ALA B 133 ARG B 136 LEU B 170 SITE 2 AC1 8 CYS B 173 GLU B 174 GLU B 178 MET B 179 CRYST1 45.800 48.400 70.100 90.00 90.00 90.00 P 21 21 21 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 0.021834 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020661 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014265 0.00000