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- PDB-1vok: ARABIDOPSIS THALIANA TBP (DIMER) -

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Basic information

Entry
Database: PDB / ID: 1vok
TitleARABIDOPSIS THALIANA TBP (DIMER)
ComponentsTATA-BOX-BINDING PROTEIN
KeywordsTRANSCRIPTION FACTOR / TRANSCRIPTION INITIATION / DNA BINDING
Function / homology
Function and homology information


DNA-templated transcription initiation / DNA binding / nucleus
Similarity search - Function
TATA-Binding Protein / TATA-box binding protein, eukaryotic / TATA-box binding protein / TATA-box binding protein, conserved site / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. / TATA-Binding Protein / TBP domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
TATA-box-binding protein 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsNikolov, D.B. / Burley, S.K.
CitationJournal: Nat.Struct.Biol. / Year: 1994
Title: 2.1 A resolution refined structure of a TATA box-binding protein (TBP).
Authors: Nikolov, D.B. / Burley, S.K.
History
DepositionApr 29, 1996Processing site: BNL
Revision 1.0Nov 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_database_status / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TATA-BOX-BINDING PROTEIN
B: TATA-BOX-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8973
Polymers44,8012
Non-polymers961
Water5,152286
1
A: TATA-BOX-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)22,4001
Polymers22,4001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TATA-BOX-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4962
Polymers22,4001
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: TATA-BOX-BINDING PROTEIN
B: TATA-BOX-BINDING PROTEIN
hetero molecules

A: TATA-BOX-BINDING PROTEIN
B: TATA-BOX-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,7946
Polymers89,6014
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_545y+1/2,x-1/2,-z+1/21
Buried area7780 Å2
ΔGint-67 kcal/mol
Surface area34800 Å2
MethodPISA
4
A: TATA-BOX-BINDING PROTEIN
B: TATA-BOX-BINDING PROTEIN
hetero molecules

A: TATA-BOX-BINDING PROTEIN
B: TATA-BOX-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,7946
Polymers89,6014
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565x,-y+3/2,-z+1/41
Buried area8850 Å2
ΔGint-69 kcal/mol
Surface area33730 Å2
MethodPISA
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-32 kcal/mol
Surface area17930 Å2
MethodPISA
6
A: TATA-BOX-BINDING PROTEIN

A: TATA-BOX-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)44,8012
Polymers44,8012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565x,-y+3/2,-z+1/41
Buried area2130 Å2
ΔGint-6 kcal/mol
Surface area19300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.000, 105.000, 215.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein TATA-BOX-BINDING PROTEIN


Mass: 22400.354 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli) / References: UniProt: P28147
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 62.79 %
Crystal grow
*PLUS
Temperature: 4-20 ℃ / pH: 8.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.0 Mammonium sulfate1reservoir
220 mMHEPES1reservoir
35 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 32781 / % possible obs: 92 % / Redundancy: 3.3 % / Rsym value: 0.044
Reflection shellResolution: 2.1→2.15 Å / Rsym value: 0.132 / % possible all: 78

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementResolution: 2.1→6 Å / σ(F): 3 /
RfactorNum. reflection
Rwork0.198 -
obs0.198 28183
Refinement stepCycle: LAST / Resolution: 2.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2995 0 5 286 3286
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg1.98
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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

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