[English] 日本語
Yorodumi
- PDB-1usm: DCOH, A BIFUNCTIONAL PROTEIN-BINDING TRANSCRIPTIONAL COACTIVATOR,... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1usm
TitleDCOH, A BIFUNCTIONAL PROTEIN-BINDING TRANSCRIPTIONAL COACTIVATOR, PRO9LEU MUTANT
ComponentsHEPATOCYTE NUCLEAR FACTOR 1-ALPHA
KeywordsTRANSCRIPTIONAL STIMULATOR / DIMERIZATION COFACTOR / DEHYDRATASE / 4A-CARBINOLAMINE DEHYDRATASE / TRANSREGULATOR OF HOMEODOMAIN PROTEINS / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI / STRUCTURAL GENOMICS
Function / homology
Function and homology information


4a-hydroxytetrahydrobiopterin dehydratase / 4-alpha-hydroxytetrahydrobiopterin dehydratase activity / tetrahydrobiopterin biosynthetic process
Similarity search - Function
Transcriptional coactivator/pterin dehydratase / Pterin 4 alpha carbinolamine dehydratase / Pterin 4 alpha carbinolamine dehydratase superfamily / Pterin 4 alpha carbinolamine dehydratase / Gyrase A; domain 2 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
4a-hydroxytetrahydrobiopterin dehydratase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsTahirov, T.H. / Inagaki, E.
CitationJournal: To be Published
Title: Crystal Structure of Transcriptional Coactivator DCoH from Thermus Thermophilus
Authors: Tahirov, T.H. / Inagaki, E.
History
DepositionNov 26, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA


Theoretical massNumber of molelcules
Total (without water)9,5091
Polymers9,5091
Non-polymers00
Water2,648147
1
A: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA

A: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA


Theoretical massNumber of molelcules
Total (without water)19,0172
Polymers19,0172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)55.625, 55.625, 125.882
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

-
Components

#1: Protein HEPATOCYTE NUCLEAR FACTOR 1-ALPHA / DCOH


Mass: 9508.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: DIMERIZATION DOMAIN / Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P83819*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RESIDUE PROLINE AT POSITION 9 WAS MUTATED TO LEU

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.4 %
Crystal growMethod: microbatch / pH: 5.3
Details: MICROBATCH METHOD UNDER OIL BY CRYSTALLIZATION ROBOT TERA. 25.6 MG/ML OF PROTEIN SOLUTION WAS MIXED WITH 3.15M SODIUM FORMATE AND 0.1M SODIUM ACETATE BUFFER, PH 4.0. FINAL PH WAS 5.3. ...Details: MICROBATCH METHOD UNDER OIL BY CRYSTALLIZATION ROBOT TERA. 25.6 MG/ML OF PROTEIN SOLUTION WAS MIXED WITH 3.15M SODIUM FORMATE AND 0.1M SODIUM ACETATE BUFFER, PH 4.0. FINAL PH WAS 5.3. CRYOPROTECTANT CONTENT WAS: 25% GLYCEROL, 2.0M SODIUM FORMATE, AND 0.6M SODIUM ACETATE BUFFER, PH 4.0.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.8
DetectorType: RIGAKU IMAGE PLATE RAXIS-V / Detector: IMAGE PLATE / Date: Feb 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.2→20 Å / Num. obs: 30991 / % possible obs: 98.7 % / Observed criterion σ(I): -0.2 / Redundancy: 8.7 % / Biso Wilson estimate: 12.1 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 41.4
Reflection shellResolution: 1.2→1.22 Å / Rmerge(I) obs: 0.146 / Mean I/σ(I) obs: 11.7 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DCO

1dco


Resolution: 1.2→18.77 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3515920.09 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESIDUES 7-9 ARE DISORDERED AND NOT INCLUDED IN THE MODEL
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1539 5 %RANDOM
Rwork0.215 ---
obs0.215 30967 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.4998 Å2 / ksol: 0.393311 e/Å3
Displacement parametersBiso mean: 19.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å20 Å2
2---0.86 Å20 Å2
3---1.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.2→18.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms646 0 0 147 793
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.811.5
X-RAY DIFFRACTIONc_mcangle_it2.522
X-RAY DIFFRACTIONc_scbond_it3.652
X-RAY DIFFRACTIONc_scangle_it5.032.5
LS refinement shellResolution: 1.2→1.28 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.255 251 4.9 %
Rwork0.246 4839 -
obs--99.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

+
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