[English] 日本語
Yorodumi
- PDB-6onc: Crystal structure of Desulfovibrio vulgaris carbon monoxide dehyd... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6onc
TitleCrystal structure of Desulfovibrio vulgaris carbon monoxide dehydrogenase produced without CooC, as-isolated
ComponentsCarbon monoxide dehydrogenase
KeywordsOXIDOREDUCTASE / nickel-iron-sulfur (Ni-Fe-S) cluster / iron-sulfur (Fe-S) cluster / metalloenzyme
Function / homology
Function and homology information


anaerobic carbon monoxide dehydrogenase / hydroxylamine reductase activity / anaerobic carbon-monoxide dehydrogenase activity / nickel cation binding / generation of precursor metabolites and energy / peroxidase activity / response to hydrogen peroxide / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #30 / Rossmann fold - #2030 / 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 / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #30 / Rossmann fold - #2030 / 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 / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / FE2/S2 (INORGANIC) CLUSTER / IRON/SULFUR CLUSTER / FE(4)-NI(1)-S(4) CLUSTER / Carbon monoxide dehydrogenase
Similarity search - Component
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsWittenborn, E.C. / Cohen, S.E. / Drennan, C.L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM069857 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM126982 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM008334 United States
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Structural insight into metallocofactor maturation in carbon monoxide dehydrogenase.
Authors: Wittenborn, E.C. / Cohen, S.E. / Merrouch, M. / Leger, C. / Fourmond, V. / Dementin, S. / Drennan, C.L.
History
DepositionApr 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carbon monoxide dehydrogenase
B: Carbon monoxide dehydrogenase
C: Carbon monoxide dehydrogenase
D: Carbon monoxide dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)275,02831
Polymers270,8644
Non-polymers4,16527
Water48,1542673
1
A: Carbon monoxide dehydrogenase
B: Carbon monoxide dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,44414
Polymers135,4322
Non-polymers2,01212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10570 Å2
ΔGint-198 kcal/mol
Surface area36190 Å2
MethodPISA
2
C: Carbon monoxide dehydrogenase
D: Carbon monoxide dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,58417
Polymers135,4322
Non-polymers2,15315
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10860 Å2
ΔGint-209 kcal/mol
Surface area36360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.790, 144.150, 123.690
Angle α, β, γ (deg.)90.00, 98.50, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Carbon monoxide dehydrogenase


Mass: 67715.898 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Gene: cooS, DVU_2098 / Production host: Desulfovibrio fructosivorans (bacteria)
References: UniProt: Q72A99, anaerobic carbon monoxide dehydrogenase

-
Non-polymers , 8 types, 2700 molecules

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


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical
ChemComp-XCC / FE(4)-NI(1)-S(4) CLUSTER / C CLUSTER


Mass: 410.333 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4NiS4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2673 / 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: 2.11 Å3/Da / Density % sol: 41.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 200-275 mM magnesium chloride, 14-20% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 11, 2017
RadiationMonochromator: Cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.5→100 Å / Num. obs: 338890 / % possible obs: 95 % / Redundancy: 6.5 % / Rsym value: 0.092 / Net I/σ(I): 11.5
Reflection shellResolution: 1.5→1.53 Å / Num. unique obs: 24577 / Rsym value: 0.904

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6B6V

6b6v


Resolution: 1.5→93.272 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.68
RfactorNum. reflection% reflection
Rfree0.1784 17181 5.07 %
Rwork0.1538 --
obs0.1551 338811 94.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→93.272 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18426 0 104 2673 21203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00719445
X-RAY DIFFRACTIONf_angle_d0.93226564
X-RAY DIFFRACTIONf_dihedral_angle_d25.8857188
X-RAY DIFFRACTIONf_chiral_restr0.0793083
X-RAY DIFFRACTIONf_plane_restr0.0053517
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4996-1.51660.28525080.24999720X-RAY DIFFRACTION86
1.5166-1.53450.27955580.249810508X-RAY DIFFRACTION93
1.5345-1.55320.2625570.23210565X-RAY DIFFRACTION94
1.5532-1.57280.26295680.226310707X-RAY DIFFRACTION95
1.5728-1.59350.24645770.212210725X-RAY DIFFRACTION95
1.5935-1.61540.24665740.207810776X-RAY DIFFRACTION95
1.6154-1.63850.23675700.202410766X-RAY DIFFRACTION96
1.6385-1.66290.23725870.197810773X-RAY DIFFRACTION95
1.6629-1.68890.20645670.184410756X-RAY DIFFRACTION96
1.6889-1.71660.21545740.182410777X-RAY DIFFRACTION95
1.7166-1.74620.20745720.178710748X-RAY DIFFRACTION95
1.7462-1.77790.20285820.174410811X-RAY DIFFRACTION96
1.7779-1.81210.20035580.176710431X-RAY DIFFRACTION93
1.8121-1.84910.20525660.1710541X-RAY DIFFRACTION93
1.8491-1.88940.19965760.159310914X-RAY DIFFRACTION97
1.8894-1.93330.18885860.157310892X-RAY DIFFRACTION97
1.9333-1.98170.19785800.156110889X-RAY DIFFRACTION96
1.9817-2.03520.18445790.149310869X-RAY DIFFRACTION96
2.0352-2.09510.17685840.148610913X-RAY DIFFRACTION96
2.0951-2.16280.17945820.145310853X-RAY DIFFRACTION96
2.1628-2.24010.18025850.144510748X-RAY DIFFRACTION95
2.2401-2.32980.16615480.143310103X-RAY DIFFRACTION89
2.3298-2.43580.16585490.141611073X-RAY DIFFRACTION98
2.4358-2.56420.17396090.143410978X-RAY DIFFRACTION97
2.5642-2.72490.17156260.144510998X-RAY DIFFRACTION97
2.7249-2.93530.16945920.145610933X-RAY DIFFRACTION96
2.9353-3.23070.17025480.144210673X-RAY DIFFRACTION94
3.2307-3.69820.14875770.134310469X-RAY DIFFRACTION93
3.6982-4.65940.13755690.124711059X-RAY DIFFRACTION97
4.6594-93.45330.16485730.155210662X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: 15.3256 Å / Origin y: 20.0899 Å / Origin z: -16.3804 Å
111213212223313233
T0.1333 Å20.0023 Å20.0023 Å2-0.1526 Å20.0056 Å2--0.1924 Å2
L0.0517 °2-0.0055 °20.0234 °2-0.0501 °20.0037 °2--0.102 °2
S0.011 Å °-0.0034 Å °-0.0003 Å °0.003 Å °0.0081 Å °0.0011 Å °-0.0071 Å °-0.0178 Å °-0.0194 Å °
Refinement TLS groupSelection details: all

+
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