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- PDB-1mp9: TBP from a mesothermophilic archaeon, Sulfolobus acidocaldarius -

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Basic information

Entry
Database: PDB / ID: 1mp9
TitleTBP from a mesothermophilic archaeon, Sulfolobus acidocaldarius
ComponentsTATA-binding protein
KeywordsDNA BINDING PROTEIN / TRANSCRIPTION REGULATION / DNA-BINDING PROTEIN / TRANSCRIPTION FACTOR
Function / homology
Function and homology information


DNA-templated transcription initiation / DNA-binding transcription factor activity / DNA binding
Similarity search - Function
TATA-box binding protein, archaea / TATA-Binding Protein / 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
TATA-box-binding protein
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKoike, H. / Kawashima-Ohya, Y. / Yamasaki, T. / Clowney, L. / Katsuya, Y. / Suzuki, M.
CitationJournal: Structure / Year: 2004
Title: Origins of Protein Stability Revealed by Comparing Crystal Structures of TATA Binding Proteins.
Authors: Koike, H. / Kawashima-Ohya, Y. / Yamasaki, T. / Clowney, L. / Katsuya, Y. / Suzuki, M.
History
DepositionSep 12, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Mar 13, 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-binding protein
B: TATA-binding protein


Theoretical massNumber of molelcules
Total (without water)44,9972
Polymers44,9972
Non-polymers00
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-15 kcal/mol
Surface area20980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.900, 80.400, 86.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-308-

HOH

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Components

#1: Protein TATA-binding protein / box A binding protein


Mass: 22498.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Plasmid: pET21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9UWN7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.51 Å3/Da / Density % sol: 50.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: lithium sulfate, ammonium sulfate, citrate, 2-propanol, glycerol, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.1 Mcitrate1reservoirpH5.6
21.0 M1reservoirLi2SO4
30.75 Mammonium sulfate1reservoir
42 %2-propanol1reservoir
530 %(v/v)glycerol1reservoir
610 mg/mlprotein1drop
70.1 MHEPES1droppH7.0
80.6 M1dropKCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU / Wavelength: 0.834 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 21, 1999
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.834 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 61045 / Num. obs: 31120 / % possible obs: 94.9 % / Observed criterion σ(F): 0.2 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.051
Reflection shellResolution: 2→2.2 Å / % possible all: 98.4

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→10 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1501 -random
Rwork0.209 ---
obs0.209 29466 94.8 %-
all-29660 --
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3028 0 0 305 3333
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d1
LS refinement shellResolution: 2→2.074 Å
RfactorNum. reflection
Rfree0.273 134
Rwork0.195 -
obs-2702
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1

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