HEADER TRANSCRIPTION/DNA 13-FEB-96 1TGH TITLE TATA BINDING PROTEIN (TBP)/DNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*TP*AP*TP*AP*TP*AP*TP*AP*CP*G)-3'); COMPND 3 CHAIN: B, C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: PROTEIN (TATA BINDING PROTEIN (TBP)); COMPND 7 CHAIN: A; COMPND 8 SYNONYM: HTBP; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 5 ORGANISM_COMMON: HUMAN; SOURCE 6 ORGANISM_TAXID: 9606; SOURCE 7 GENE: TBP; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI K12; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 83333; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: K12; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PET21D KEYWDS TRANSCRIPTION FACTOR, DNA BINDING PROTEIN, DNA, TRANSCRIPTION-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Z.S.JUO,R.E.DICKERSON REVDAT 4 14-FEB-24 1TGH 1 SEQADV REVDAT 3 24-FEB-09 1TGH 1 VERSN REVDAT 2 01-APR-03 1TGH 1 JRNL REVDAT 1 01-AUG-96 1TGH 0 JRNL AUTH Z.S.JUO,T.K.CHIU,P.M.LEIBERMAN,I.BAIKALOV,A.J.BERK, JRNL AUTH 2 R.E.DICKERSON JRNL TITL HOW PROTEINS RECOGNIZE THE TATA BOX. JRNL REF J.MOL.BIOL. V. 261 239 1996 JRNL REFN ISSN 0022-2836 JRNL PMID 8757291 JRNL DOI 10.1006/JMBI.1996.0456 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.L.KIM,S.K.BURLEY REMARK 1 TITL 1.9 A RESOLUTION REFINED STRUCTURE OF TBP RECOGNIZING THE REMARK 1 TITL 2 MINOR GROOVE OF TATAAAAG REMARK 1 REF NAT.STRUCT.BIOL. V. 1 638 1994 REMARK 1 REFN ISSN 1072-8368 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.L.KIM,D.B.NIKOLOV,S.K.BURLEY REMARK 1 TITL CO-CRYSTAL STRUCTURE OF TBP RECOGNIZING THE MINOR GROOVE OF REMARK 1 TITL 2 A TATA ELEMENT REMARK 1 REF NATURE V. 365 520 1993 REMARK 1 REFN ISSN 0028-0836 REMARK 2 REMARK 2 RESOLUTION. 2.90 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 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 : 9013 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.294 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : 1429 REMARK 3 NUCLEIC ACID ATOMS : 486 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 18 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) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 2.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.490 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: NULL REMARK 4 REMARK 4 1TGH 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_1000176666. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-APR-95 REMARK 200 TEMPERATURE (KELVIN) : 92.00 REMARK 200 PH : 8.00 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 8.00 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 33.48250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.11300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.69850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.11300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.48250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.69850 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 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 GLY A 151 REMARK 465 SER A 152 REMARK 465 ARG A 153 REMARK 465 GLY A 154 REMARK 465 THR A 335 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 O2 DC B 111 H22 DG C 114 1.54 REMARK 500 H3 DT B 103 N1 DA C 122 1.58 REMARK 500 H3 DT B 109 N1 DA C 116 1.60 REMARK 500 H22 DG B 102 O2 DC C 123 1.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DC B 101 O5' - C5' - C4' ANGL. DEV. = -5.0 DEGREES REMARK 500 PRO A 243 C - N - CA ANGL. DEV. = 10.7 DEGREES REMARK 500 PRO A 281 C - N - CA ANGL. DEV. = 10.7 DEGREES 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 CYS A 172 116.05 175.17 REMARK 500 ARG A 184 -45.13 56.50 REMARK 500 ASN A 189 88.66 -159.64 REMARK 500 PRO A 190 -1.11 -54.77 REMARK 500 GLU A 202 116.81 -163.90 REMARK 500 ARG A 204 106.70 -49.13 REMARK 500 ALA A 220 179.94 -38.95 REMARK 500 LYS A 221 14.49 -144.99 REMARK 500 PRO A 243 70.17 -63.66 REMARK 500 LYS A 261 56.01 72.36 REMARK 500 PHE A 262 148.57 165.47 REMARK 500 HIS A 273 22.04 -140.07 REMARK 500 ARG A 295 82.56 -68.54 REMARK 500 ARG A 314 -39.09 -39.10 REMARK 500 REMARK 500 REMARK: NULL DBREF 1TGH A 151 335 UNP P20226 TBP_HUMAN 113 297 DBREF 1TGH B 101 112 PDB 1TGH 1TGH 101 112 DBREF 1TGH C 113 124 PDB 1TGH 1TGH 113 124 SEQADV 1TGH GLY A 151 UNP P20226 ALA 113 CONFLICT SEQADV 1TGH ARG A 153 UNP P20226 GLU 115 CONFLICT SEQADV 1TGH GLY A 154 UNP P20226 SER 116 CONFLICT SEQRES 1 B 12 DC DG DT DA DT DA DT DA DT DA DC DG SEQRES 1 C 12 DC DG DT DA DT DA DT DA DT DA DC DG SEQRES 1 A 185 GLY SER ARG GLY SER GLY ILE VAL PRO GLN LEU GLN ASN SEQRES 2 A 185 ILE VAL SER THR VAL ASN LEU GLY CYS LYS LEU ASP LEU SEQRES 3 A 185 LYS THR ILE ALA LEU ARG ALA ARG ASN ALA GLU TYR ASN SEQRES 4 A 185 PRO LYS ARG PHE ALA ALA VAL ILE MET ARG ILE ARG GLU SEQRES 5 A 185 PRO ARG THR THR ALA LEU ILE PHE SER SER GLY LYS MET SEQRES 6 A 185 VAL CYS THR GLY ALA LYS SER GLU GLU GLN SER ARG LEU SEQRES 7 A 185 ALA ALA ARG LYS TYR ALA ARG VAL VAL GLN LYS LEU GLY SEQRES 8 A 185 PHE PRO ALA LYS PHE LEU ASP PHE LYS ILE GLN ASN MET SEQRES 9 A 185 VAL GLY SER CYS ASP VAL LYS PHE PRO ILE ARG LEU GLU SEQRES 10 A 185 GLY LEU VAL LEU THR HIS GLN GLN PHE SER SER TYR GLU SEQRES 11 A 185 PRO GLU LEU PHE PRO GLY LEU ILE TYR ARG MET ILE LYS SEQRES 12 A 185 PRO ARG ILE VAL LEU LEU ILE PHE VAL SER GLY LYS VAL SEQRES 13 A 185 VAL LEU THR GLY ALA LYS VAL ARG ALA GLU ILE TYR GLU SEQRES 14 A 185 ALA PHE GLU ASN ILE TYR PRO ILE LEU LYS GLY PHE ARG SEQRES 15 A 185 LYS THR THR FORMUL 4 HOH *18(H2 O) HELIX 1 1 LEU A 176 ARG A 182 1 7 HELIX 2 2 GLU A 223 GLY A 241 1 19 HELIX 3 3 LEU A 266 THR A 272 1 7 HELIX 4 4 ARG A 314 PHE A 331 1 18 SHEET 1 A 5 SER A 166 ASN A 169 0 SHEET 2 A 5 LYS A 214 THR A 218 -1 N CYS A 217 O SER A 166 SHEET 3 A 5 THR A 206 PHE A 210 -1 N LEU A 208 O VAL A 216 SHEET 4 A 5 ALA A 195 MET A 198 -1 N MET A 198 O ALA A 207 SHEET 5 A 5 ALA A 186 TYR A 188 -1 N GLU A 187 O ILE A 197 SHEET 1 B 5 GLY A 286 ARG A 290 0 SHEET 2 B 5 VAL A 297 PHE A 301 -1 N ILE A 300 O LEU A 287 SHEET 3 B 5 LYS A 305 THR A 309 -1 N THR A 309 O VAL A 297 SHEET 4 B 5 ASN A 253 ASP A 259 -1 N CYS A 258 O VAL A 306 SHEET 5 B 5 GLN A 160 VAL A 165 -1 N VAL A 165 O ASN A 253 CISPEP 1 GLU A 202 PRO A 203 0 0.04 CISPEP 2 LYS A 293 PRO A 294 0 0.13 CRYST1 66.965 67.397 86.226 90.00 90.00 90.00 P 21 21 21 8 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 0.014933 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014837 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011597 0.00000