[English] 日本語
Yorodumi
- PDB-9fpo: Ni,Fe-CODH : Eu(II)-reduced pH 6.0 + CO -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9fpo
TitleNi,Fe-CODH : Eu(II)-reduced pH 6.0 + CO
ComponentsCarbon monoxide dehydrogenase 2
KeywordsOXIDOREDUCTASE / C-CLUSTER / 4FE-4S / IRON / IRON-SULFUR / METAL-BINDING / NICKEL / NICKEL REDOX / CARBON DIOXIDE / CARBON MONOXIDE / CODH
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 / 4 iron, 4 sulfur cluster binding / plasma membrane / cytoplasm
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
CARBON MONOXIDE / CARBON DIOXIDE / FE3-S4 CLUSTER / : / FE2/S2 (INORGANIC) CLUSTER / NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / IRON/SULFUR CLUSTER / Carbon monoxide dehydrogenase 2
Similarity search - Component
Biological speciesCarboxydothermus hydrogenoformans Z-2901 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.03 Å
AuthorsBasak, Y. / Jeoung, J.-H. / Dobbek, H.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)DO 785/6-2 Germany
Germanys Excellence StrategyEXC 2008 - 390540038 - UniSysCat Germany
CitationJournal: Nature Catalysis / Year: 2025
Title: Ni,Fe-CODH : Ti(III)-reduced pH 8.0
Authors: Basak, Y. / Jeoung, J.-H. / Dobbek, H.
History
DepositionJun 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
X: Carbon monoxide dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,25910
Polymers67,0201
Non-polymers1,2389
Water14,880826
1
X: Carbon monoxide dehydrogenase 2
hetero molecules

X: Carbon monoxide dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,51720
Polymers134,0412
Non-polymers2,47618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area10700 Å2
ΔGint-218 kcal/mol
Surface area38440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.208, 75.363, 71.119
Angle α, β, γ (deg.)90.00, 111.39, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11X-1247-

HOH

21X-1751-

HOH

-
Components

-
Protein , 1 types, 1 molecules X

#1: Protein Carbon monoxide dehydrogenase 2 / CODH 2


Mass: 67020.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans Z-2901 (bacteria)
Strain: Z-2901 / DSM 6008 / Gene: cooS2, cooSII, CHY_0085 / Plasmid: PET28A / Production host: Escherichia coli B (bacteria) / Strain (production host): ROSSETTA DE3
References: UniProt: Q9F8A8, anaerobic carbon monoxide dehydrogenase

-
Non-polymers , 10 types, 835 molecules

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


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#4: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#10: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 826 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.21 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES pH 7.5, PEG 2000MME 14-18%

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Feb 2, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.03→66.38 Å / Num. obs: 273224 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rrim(I) all: 0.099 / Net I/σ(I): 9.3
Reflection shellResolution: 1.03→1.06 Å / Num. unique obs: 27175 / CC1/2: 0.427

-
Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
MxCuBEdata collection
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.03→33.11 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1454 13522 4.96 %
Rwork0.1269 --
obs0.1278 272869 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.03→33.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4659 0 41 826 5526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115256
X-RAY DIFFRACTIONf_angle_d1.4537221
X-RAY DIFFRACTIONf_dihedral_angle_d13.1221990
X-RAY DIFFRACTIONf_chiral_restr1.453846
X-RAY DIFFRACTIONf_plane_restr0.013952
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.03-1.040.31134180.29118283X-RAY DIFFRACTION96
1.04-1.050.28674460.27588471X-RAY DIFFRACTION98
1.05-1.060.27974660.26568526X-RAY DIFFRACTION99
1.06-1.080.26884610.25648672X-RAY DIFFRACTION100
1.08-1.090.24294230.24058664X-RAY DIFFRACTION100
1.09-1.110.24324680.22928583X-RAY DIFFRACTION100
1.11-1.120.23684510.22338681X-RAY DIFFRACTION100
1.12-1.140.21364310.2058632X-RAY DIFFRACTION100
1.14-1.160.21544410.19328640X-RAY DIFFRACTION100
1.16-1.180.18934300.17858632X-RAY DIFFRACTION100
1.18-1.20.17744750.16948637X-RAY DIFFRACTION100
1.2-1.220.19834560.16578662X-RAY DIFFRACTION100
1.22-1.240.17664540.15678626X-RAY DIFFRACTION100
1.24-1.270.18054880.15448613X-RAY DIFFRACTION100
1.27-1.290.18244110.15038676X-RAY DIFFRACTION100
1.29-1.320.1554640.14138695X-RAY DIFFRACTION100
1.32-1.360.1544260.13658633X-RAY DIFFRACTION100
1.36-1.390.15914710.12798655X-RAY DIFFRACTION100
1.39-1.430.144360.11868712X-RAY DIFFRACTION100
1.43-1.480.1234210.10948675X-RAY DIFFRACTION100
1.48-1.530.12214960.09918617X-RAY DIFFRACTION100
1.53-1.60.10914690.09328621X-RAY DIFFRACTION100
1.6-1.670.10924760.08948661X-RAY DIFFRACTION100
1.67-1.760.1054480.09158688X-RAY DIFFRACTION100
1.76-1.870.11094860.09448663X-RAY DIFFRACTION100
1.87-2.010.11974270.0968686X-RAY DIFFRACTION100
2.01-2.210.11574090.10038765X-RAY DIFFRACTION100
2.21-2.530.11584430.09898713X-RAY DIFFRACTION100
2.53-3.190.13214560.11088730X-RAY DIFFRACTION100
3.19-33.110.14084750.12148835X-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