[English] 日本語
Yorodumi
- PDB-1pcz: STRUCTURE OF TATA-BINDING PROTEIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pcz
TitleSTRUCTURE OF TATA-BINDING PROTEIN
ComponentsTATA-BINDING PROTEIN
KeywordsDNA BINDING PROTEIN / TRANSCRIPTION REGULATION / DNA-BINDING PROTEIN / NUCLEAR PROTEIN
Function / homology
Function and homology information


general transcription initiation factor activity / 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 speciesPyrococcus woesei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 Å
AuthorsDedecker, B.S. / Sigler, P.B.
CitationJournal: J.Mol.Biol. / Year: 1996
Title: The crystal structure of a hyperthermophilic archaeal TATA-box binding protein.
Authors: DeDecker, B.S. / O'Brien, R. / Fleming, P.J. / Geiger, J.H. / Jackson, S.P. / Sigler, P.B.
History
DepositionOct 4, 1996Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_keywords.text

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TATA-BINDING PROTEIN
B: TATA-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)42,6762
Polymers42,6762
Non-polymers00
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-14 kcal/mol
Surface area16410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.620, 89.620, 141.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein TATA-BINDING PROTEIN / TBP


Mass: 21337.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus woesei (archaea) / Cell line: BL21 / Plasmid: PET 11A (NOVAGEN) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P62001
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.2 Å3/Da / Density % sol: 71 %
Crystal growpH: 7.5
Details: 50% SATURATED AMMONIUM SULFATE, 0.1 M TRIS PH 7.5, 0.1 M KCL
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
2100 mMTris-HCl1drop
3100 mM1dropKCl
425 %satammonium sulfate1drop
5100 mMTris-HCl1reservoir
6100 mM1reservoirKCl
750 %satammonium sulfate1reservoir

-
Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.95
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Oct 4, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 36912 / % possible obs: 98.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 43.5 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 16.9
Reflection shellResolution: 2.2→2.33 Å / Redundancy: 3 % / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 4.5 / % possible all: 98.6
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / % possible obs: 98.6 %

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-96model building
X-PLOR3.843refinement
SHELXL-96phasing
RefinementMethod to determine structure: MIR / Resolution: 2.2→6 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.3 3147 10.2 %RANDOM
Rwork0.218 ---
obs0.218 30707 99.1 %-
Displacement parametersBiso mean: 43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.31 Å
Luzzati d res low-6 Å
Luzzati sigma a0.41 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2854 0 0 268 3122
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.69
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.011.5
X-RAY DIFFRACTIONx_mcangle_it4.692
X-RAY DIFFRACTIONx_scbond_it5.382
X-RAY DIFFRACTIONx_scangle_it8.32.5
LS refinement shellResolution: 2.2→2.33 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.398 521 10.3 %
Rwork0.365 4529 -
obs--98.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 6 Å / Num. reflection obs: 27565 / Rfactor Rfree: 0.301
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.85
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.69

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more