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- PDB-1vto: 1.9 A RESOLUTION REFINED STRUCTURE OF TBP RECOGNIZING THE MINOR G... -

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Basic information

Entry
Database: PDB / ID: 1vto
Title1.9 A RESOLUTION REFINED STRUCTURE OF TBP RECOGNIZING THE MINOR GROOVE OF TATAAAAG
Components
  • DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*CP*A)-3')
  • DNA (5'-D(*TP*GP*CP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*C)-3')
  • TATA BINDING PROTEINTATA-binding protein
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / KINKED / TRANSCRIPTION-DNA complex
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-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. / TBP domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / TATA-box-binding protein 1
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsKim, J.L. / Burley, S.K.
CitationJournal: Nat.Struct.Biol. / Year: 1994
Title: 1.9 A Resolution Refined Structure of TBP Recognizing the Minor Groove of TATAAAAG
Authors: Kim, J.L. / Burley, S.K.
History
DepositionSep 6, 1996Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Mar 13, 2024Group: Source and taxonomy / Category: entity_src_nat / pdbx_entity_src_syn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*CP*A)-3')
D: DNA (5'-D(*TP*GP*CP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*C)-3')
E: DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*CP*A)-3')
F: DNA (5'-D(*TP*GP*CP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*C)-3')
A: TATA BINDING PROTEIN
B: TATA BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)59,8546
Polymers59,8546
Non-polymers00
Water9,386521
1
C: DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*CP*A)-3')
D: DNA (5'-D(*TP*GP*CP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*C)-3')
A: TATA BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)29,9273
Polymers29,9273
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-18 kcal/mol
Surface area12650 Å2
MethodPISA
2
E: DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*CP*A)-3')
F: DNA (5'-D(*TP*GP*CP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*C)-3')
B: TATA BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)29,9273
Polymers29,9273
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-15 kcal/mol
Surface area12870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.000, 147.000, 57.000
Angle α, β, γ (deg.)90.00, 90.50, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

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


Mass: 4337.855 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)
#2: DNA chain DNA (5'-D(*TP*GP*CP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*C)-3')


Mass: 4221.751 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)
#3: Protein TATA BINDING PROTEIN / TATA-binding protein / TRANSCRIPTION INITIATION FACTOR TFIID-1 / TATA-BOX FACTOR 1 / TBP-1


Mass: 21367.279 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ARABIDOPSIS THALIANA (thale cress) / Species: THALIANA / References: UniProt: P28147
#4: Water ChemComp-HOH / water / TRANSCRIPTION INITIATION FACTOR TFIID-1 / TATA-BOX FACTOR 1 / TBP-1 / Water


Mass: 18.015 Da / Num. of mol.: 521 / Source method: isolated from a natural source / Formula: H2O

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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: 2.94 Å3/Da / Density % sol: 58.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.2 / Details: pH 6.20, VAPOR DIFFUSION, temperature 277.00K
Components of the solutions
IDConc.NameCrystal-IDDetailsSol-IDVolume (Å3)
12 WATER1311
25 DTT1614
38 GLYCEROL1917
411 MES112110
514 KCL115113
617 NH4 ACETATE118116
720 WATER121219
823 DTT124222
926 GLYCEROL127225
1029 MES130228

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25
DetectorType: FUJI / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.88→20 Å / Num. obs: 51793 / % possible obs: 93.2 % / Rsym value: 5.2

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Processing

Software
NameClassification
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.9→6 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.264 --random
Rwork0.194 ---
obs0.194 49515 94.4 %-
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2956 1134 0 521 4611
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.57
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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