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- PDB-1ais: TATA-BINDING PROTEIN/TRANSCRIPTION FACTOR (II)B/TATA-BOX COMPLEX ... -

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Basic information

Entry
Database: PDB / ID: 1ais
TitleTATA-BINDING PROTEIN/TRANSCRIPTION FACTOR (II)B/TATA-BOX COMPLEX FROM PYROCOCCUS WOESEI
Components
  • DNA (5'-D(*AP*AP*CP*TP*TP*AP*CP*TP*TP*TP*(5IU)P*(5IU)P*AP*AP*AP*GP*C)-3')
  • DNA (5'-D(*GP*CP*TP*TP*TP*AP*AP*AP*AP*AP*GP*TP*AP*AP*GP*TP*T )-3')
  • PROTEIN (TATA-BINDING PROTEIN)
  • PROTEIN (TRANSCRIPTION INITIATION FACTOR IIB)
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION / HYPERTHERMOPHILE / RIBOSOME BINDING / COMPLEX (RIBOSOME BINDING- DNA) / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


transcription preinitiation complex assembly / transcription preinitiation complex / TBP-class protein binding / DNA-templated transcription initiation / DNA-binding transcription factor activity / DNA binding / zinc ion binding
Similarity search - Function
Transcription initiation factor TFIIB, archaea / TATA-box binding protein, archaea / TATA-Binding Protein / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Cyclin-like / Zinc finger TFIIB-type profile. / Transcription factor TFIIB ...Transcription initiation factor TFIIB, archaea / TATA-box binding protein, archaea / TATA-Binding Protein / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Cyclin-like / Zinc finger TFIIB-type profile. / Transcription factor TFIIB / Zinc finger, TFIIB-type / TFIIB zinc-binding / TATA-Binding Protein / TATA-box binding protein / TATA-box binding protein, conserved site / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. / Cyclin A; domain 1 / TBP domain superfamily / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcription initiation factor IIB / TATA-box-binding protein
Similarity search - Component
Biological speciesPyrococcus woesei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.1 Å
AuthorsKosa, P.F. / Ghosh, G. / Dedecker, B.S. / Sigler, P.B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: The 2.1-A crystal structure of an archaeal preinitiation complex: TATA-box-binding protein/transcription factor (II)B core/TATA-box.
Authors: Kosa, P.F. / Ghosh, G. / DeDecker, B.S. / Sigler, P.B.
History
DepositionApr 24, 1997Deposition site: BNL / Processing site: NDB
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*AP*AP*CP*TP*TP*AP*CP*TP*TP*TP*(5IU)P*(5IU)P*AP*AP*AP*GP*C)-3')
E: DNA (5'-D(*GP*CP*TP*TP*TP*AP*AP*AP*AP*AP*GP*TP*AP*AP*GP*TP*T )-3')
A: PROTEIN (TATA-BINDING PROTEIN)
B: PROTEIN (TRANSCRIPTION INITIATION FACTOR IIB)


Theoretical massNumber of molelcules
Total (without water)53,5044
Polymers53,5044
Non-polymers00
Water5,188288
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.700, 91.200, 74.200
Angle α, β, γ (deg.)90.00, 122.70, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: DNA chain DNA (5'-D(*AP*AP*CP*TP*TP*AP*CP*TP*TP*TP*(5IU)P*(5IU)P*AP*AP*AP*GP*C)-3')


Mass: 5384.125 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*GP*CP*TP*TP*TP*AP*AP*AP*AP*AP*GP*TP*AP*AP*GP*TP*T )-3')


Mass: 5249.446 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (TATA-BINDING PROTEIN) / TBP


Mass: 20279.707 Da / Num. of mol.: 1 / Fragment: RESIDUES 1 - 181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus woesei (archaea) / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P62001
#4: Protein PROTEIN (TRANSCRIPTION INITIATION FACTOR IIB) / TFB TFIIB


Mass: 22590.379 Da / Num. of mol.: 1 / Fragment: C TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus woesei (archaea) / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P61999
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.34 Å3/Da / Density % sol: 64 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.4
Details: HANGING DROP METHOD 8% PEG 8000, 200 MM POTASSIUM PHOSPHATE PH 7.4., vapor diffusion - hanging drop
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2K PHOSPHATE11
3PEG 800011
Crystal
*PLUS
Density % sol: 64 %
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14 %(w/v)PEG80001drop
2100 mMpotassium phosphate1drop
30.15 mMDNA complex1drop
475 mMpotassium acetate1drop
55 mMTris1drop
68 %PEG80001reservoir
7200 mMpotassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1
DetectorDetector: CCD / Date: Jan 1, 1996 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 14445 / % possible obs: 92 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 4 % / Biso Wilson estimate: 31.1 Å2 / Rsym value: 0.088
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.396 / % possible all: 96.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementMethod to determine structure: MIR / Resolution: 2.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1839 5 %RANDOM
Rwork0.212 ---
obs0.212 36876 92 %-
Displacement parametersBiso mean: 36.6 Å2
Baniso -1Baniso -2Baniso -3
1--13.89 Å20 Å2-7.356 Å2
2---13.92 Å20 Å2
3----2.845 Å2
Refine analyzeLuzzati d res low obs: 40 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2951 689 2 288 3930
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.55
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.53
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor all: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 36.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.53

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