[English] 日本語
Yorodumi
- PDB-6t7j: As-isolated Ni-free crystal structure of carbon monoxide dehydrog... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6t7j
TitleAs-isolated Ni-free crystal structure of carbon monoxide dehydrogenase from Thermococcus sp. AM4 produced without CooC maturase
ComponentsCarbon monoxide dehydrogenase
KeywordsOXIDOREDUCTASE / Ni-free cluster C / CO dehydrogenase
Function / homology
Function and homology information


anaerobic carbon monoxide dehydrogenase / anaerobic carbon-monoxide dehydrogenase activity / : / nickel cation binding / generation of precursor metabolites and energy / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding
Similarity search - Function
Ni-containing CO dehydrogenase / CO dehydrogenase, alpha-bundle / Hydroxylamine reductase/Ni-containing CO dehydrogenase / Prismane/CO dehydrogenase family / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily
Similarity search - Domain/homology
(R,R)-2,3-BUTANEDIOL / CITRIC ACID / FE2/S2 (INORGANIC) CLUSTER / Broken Fe4S4 cluster / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / IRON/SULFUR CLUSTER / Carbon monoxide dehydrogenase
Similarity search - Component
Biological speciesThermococcus sp. AM4 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsDobbek, H. / Jeoung, J.-H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationEXC 2008/1 (UniSysCat) - 390540038 Germany
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2020
Title: The two CO-dehydrogenases of Thermococcus sp. AM4.
Authors: Benvenuti, M. / Meneghello, M. / Guendon, C. / Jacq-Bailly, A. / Jeoung, J.H. / Dobbek, H. / Leger, C. / Fourmond, V. / Dementin, S.
History
DepositionOct 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: 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
B: Carbon monoxide dehydrogenase
A: Carbon monoxide dehydrogenase
D: Carbon monoxide dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,09121
Polymers204,5053
Non-polymers3,58618
Water3,477193
1
B: Carbon monoxide dehydrogenase
hetero molecules

B: Carbon monoxide dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,03818
Polymers136,3372
Non-polymers2,70116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area9350 Å2
ΔGint-118 kcal/mol
Surface area39080 Å2
MethodPISA
2
A: Carbon monoxide dehydrogenase
hetero molecules

D: Carbon monoxide dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,57212
Polymers136,3372
Non-polymers2,23510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x+1/2,y+1/2,-z+11
Buried area9590 Å2
ΔGint-129 kcal/mol
Surface area37670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)268.138, 64.061, 100.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11D-851-

HOH

-
Components

-
Protein , 1 types, 3 molecules BAD

#1: Protein Carbon monoxide dehydrogenase


Mass: 68168.406 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: FS4)(FS4)(CX3)(PO4)(BU3)(BU3)(BU3)(PEG) are non-ploymers.
Source: (gene. exp.) Thermococcus sp. AM4 (archaea) / Gene: TAM4_1067 / Production host: Desulfovibrio fructosivorans (bacteria)
References: UniProt: B7R5K0, anaerobic carbon monoxide dehydrogenase

-
Non-polymers , 8 types, 211 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe2S2
#4: Chemical ChemComp-MSK / Broken Fe4S4 cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.1 M phosphate/citrate pH 4.2, 40% (w/v) polyethyleneglycol 300

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184, 1.732, 1.479
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91841
21.7321
31.4791
ReflectionResolution: 2.34→47.32 Å / Num. obs: 73992 / % possible obs: 99.3 % / Redundancy: 6.61 % / CC1/2: 0.997 / Net I/σ(I): 8.19
Reflection shellResolution: 2.34→2.48 Å / Num. unique obs: 11596 / CC1/2: 0.978

-
Processing

Software
NameVersionClassification
PHENIX1.16-3549refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B53

3b53


Resolution: 2.43→47.32 Å / Cross valid method: FREE R-VALUE /
Num. reflection% reflection
obs73986 99.3 %
Displacement parametersBiso mean: 53.52 Å2
Refinement stepCycle: LAST / Resolution: 2.43→47.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14324 0 68 193 14585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008814690
X-RAY DIFFRACTIONf_angle_d0.874519977
X-RAY DIFFRACTIONf_chiral_restr0.04782296
X-RAY DIFFRACTIONf_plane_restr0.00412531
X-RAY DIFFRACTIONf_dihedral_angle_d20.56628910

+
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