[English] 日本語
Yorodumi
- PDB-6cpb: Crystal structure of the heme domain of CooA from Carboxydothermu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6cpb
TitleCrystal structure of the heme domain of CooA from Carboxydothermus hydrogenoformans
ComponentsCarbon monoxide oxidation system transcription regulator CooA-1
KeywordsTRANSCRIPTION / CO sensing transcription regulator / Heme binding protein / DNA binding
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding / metal ion binding
Similarity search - Function
helix_turn_helix, cAMP Regulatory protein / Crp-like helix-turn-helix domain / Crp-type HTH domain profile. / Crp-type HTH domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls ...helix_turn_helix, cAMP Regulatory protein / Crp-like helix-turn-helix domain / Crp-type HTH domain profile. / Crp-type HTH domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Winged helix DNA-binding domain superfamily / Jelly Rolls / Winged helix-like DNA-binding domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Carbon monoxide oxidation system transcription regulator CooA-1
Similarity search - Component
Biological speciesCarboxydothermus hydrogenoformans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.155 Å
AuthorsTripathi, S.M. / Poulos, T.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM57353 United States
CitationJournal: Biochemistry / Year: 2018
Title: Testing the N-Terminal Velcro Model of CooA Carbon Monoxide Activation.
Authors: Tripathi, S. / Poulos, T.L.
History
DepositionMar 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carbon monoxide oxidation system transcription regulator CooA-1
B: Carbon monoxide oxidation system transcription regulator CooA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5028
Polymers32,9382
Non-polymers5646
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-74 kcal/mol
Surface area13180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.665, 65.820, 72.885
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Carbon monoxide oxidation system transcription regulator CooA-1


Mass: 16468.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans (bacteria)
Gene: cooA-1, CHY_1835 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3AB29
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.33 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 2 M ammonium sulfate, 100 mM Tris, pH 8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 11, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.15→72.88 Å / Num. obs: 109455 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.05 / Net I/σ(I): 14
Reflection shellResolution: 1.15→1.17 Å / Redundancy: 6 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 5388 / CC1/2: 0.89 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4K8F

4k8f


Resolution: 1.155→38.978 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.8
RfactorNum. reflection% reflection
Rfree0.1469 5462 5 %
Rwork0.129 --
obs0.1299 109323 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.155→38.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2196 0 33 301 2530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072378
X-RAY DIFFRACTIONf_angle_d0.9133238
X-RAY DIFFRACTIONf_dihedral_angle_d17.216879
X-RAY DIFFRACTIONf_chiral_restr0.078377
X-RAY DIFFRACTIONf_plane_restr0.005413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1549-1.16810.24571680.21773376X-RAY DIFFRACTION99
1.1681-1.18180.2281800.19933422X-RAY DIFFRACTION100
1.1818-1.19620.21441790.18573434X-RAY DIFFRACTION100
1.1962-1.21140.20881730.18043420X-RAY DIFFRACTION100
1.2114-1.22730.19651840.17633417X-RAY DIFFRACTION100
1.2273-1.24410.20281900.1693445X-RAY DIFFRACTION100
1.2441-1.26190.20841760.15833420X-RAY DIFFRACTION100
1.2619-1.28070.17752020.15523393X-RAY DIFFRACTION100
1.2807-1.30080.18341750.14993436X-RAY DIFFRACTION100
1.3008-1.32210.17131980.14143421X-RAY DIFFRACTION100
1.3221-1.34490.15271730.13213455X-RAY DIFFRACTION100
1.3449-1.36930.15441930.13293420X-RAY DIFFRACTION100
1.3693-1.39570.15521710.1263444X-RAY DIFFRACTION100
1.3957-1.42420.15231780.11763449X-RAY DIFFRACTION100
1.4242-1.45510.14641670.11293443X-RAY DIFFRACTION100
1.4551-1.4890.11641560.10083495X-RAY DIFFRACTION100
1.489-1.52620.12841460.10113470X-RAY DIFFRACTION100
1.5262-1.56750.11992070.09933437X-RAY DIFFRACTION100
1.5675-1.61360.12531800.09913462X-RAY DIFFRACTION100
1.6136-1.66570.12741670.09773442X-RAY DIFFRACTION100
1.6657-1.72520.11771960.09883484X-RAY DIFFRACTION100
1.7252-1.79430.12972130.10233405X-RAY DIFFRACTION100
1.7943-1.8760.131820.1033490X-RAY DIFFRACTION100
1.876-1.97490.12741740.1073475X-RAY DIFFRACTION100
1.9749-2.09860.1241850.10483512X-RAY DIFFRACTION100
2.0986-2.26060.12281730.11013496X-RAY DIFFRACTION100
2.2606-2.48810.11822010.1143496X-RAY DIFFRACTION100
2.4881-2.8480.14451850.13153527X-RAY DIFFRACTION100
2.848-3.58780.15921760.14153581X-RAY DIFFRACTION100
3.5878-38.99980.16862140.16293694X-RAY DIFFRACTION100

+
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