[English] 日本語
Yorodumi
- PDB-9iys: ChCODH2 A559W_V610H mutant in 2hour air exposure condition -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9iys
TitleChCODH2 A559W_V610H mutant in 2hour air exposure condition
ComponentsCarbon monoxide dehydrogenase 2
KeywordsOXIDOREDUCTASE / ELECTRON TRANSPORT
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
: / FE2/S2 (INORGANIC) CLUSTER / IRON/SULFUR CLUSTER / FE(4)-NI(1)-S(4) CLUSTER / Carbon monoxide dehydrogenase 2
Similarity search - Component
Biological speciesCarboxydothermus hydrogenoformans Z-2901 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsKong, S.Y. / Yoon, H.J. / Kim, S.M. / Lee, H.H.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Air-viable, rapid CO dehydrogenase with a selectively sealed tunnel
Authors: Kong, S.Y. / Yoon, H.J. / Kim, S.M. / Lee, H.H.
History
DepositionJul 31, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carbon monoxide dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3405
Polymers69,3461
Non-polymers9944
Water6,648369
1
A: Carbon monoxide dehydrogenase 2
hetero molecules

A: Carbon monoxide dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,67910
Polymers138,6922
Non-polymers1,9878
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8390 Å2
ΔGint-124 kcal/mol
Surface area37600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.344, 76.511, 71.103
Angle α, β, γ (deg.)90.00, 111.10, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-970-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Carbon monoxide dehydrogenase 2 / CODH 2


Mass: 69346.039 Da / Num. of mol.: 1 / Mutation: A559W,V610H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans Z-2901 (bacteria)
Strain: Z-2901 / Gene: cooS2, cooSII, CHY_0085 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9F8A8, anaerobic carbon monoxide dehydrogenase

-
Non-polymers , 5 types, 373 molecules

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


Mass: 351.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / 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-XCC / FE(4)-NI(1)-S(4) CLUSTER / C CLUSTER


Mass: 410.333 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4NiS4
#5: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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 Å3/Da / Density % sol: 38.81 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: PEG3350, Magnesium chloride, Hepes/NaOH

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 78964 / % possible obs: 98.1 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 8.7
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.651 / Num. unique obs: 3772 / % possible all: 94.7

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SU7

1su7


Resolution: 1.55→33.17 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.202 4090 5.19 %
Rwork0.175 --
obs0.176 78814 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→33.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4665 0 22 369 5056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084775
X-RAY DIFFRACTIONf_angle_d1.0816500
X-RAY DIFFRACTIONf_dihedral_angle_d6.408671
X-RAY DIFFRACTIONf_chiral_restr0.065782
X-RAY DIFFRACTIONf_plane_restr0.01838
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.570.3441840.28212066X-RAY DIFFRACTION78
1.57-1.590.26771370.25632483X-RAY DIFFRACTION94
1.59-1.610.26261370.24092551X-RAY DIFFRACTION96
1.61-1.630.25691420.23112472X-RAY DIFFRACTION95
1.63-1.650.2691540.21722545X-RAY DIFFRACTION97
1.65-1.670.23781370.20832535X-RAY DIFFRACTION96
1.67-1.70.25131420.21672550X-RAY DIFFRACTION96
1.7-1.720.24231570.20722527X-RAY DIFFRACTION97
1.72-1.750.21741190.20132582X-RAY DIFFRACTION97
1.75-1.780.23071310.19252572X-RAY DIFFRACTION97
1.78-1.820.23071330.18642569X-RAY DIFFRACTION98
1.82-1.850.23121320.19072571X-RAY DIFFRACTION98
1.85-1.890.22321340.18872607X-RAY DIFFRACTION97
1.89-1.930.23491170.20082610X-RAY DIFFRACTION98
1.93-1.970.23011300.18712593X-RAY DIFFRACTION98
1.97-2.020.24211520.18442562X-RAY DIFFRACTION98
2.02-2.080.23241620.1892599X-RAY DIFFRACTION99
2.08-2.140.1971330.17532633X-RAY DIFFRACTION99
2.14-2.210.18481420.17222620X-RAY DIFFRACTION99
2.21-2.290.22681480.17952643X-RAY DIFFRACTION99
2.29-2.380.17741480.17132611X-RAY DIFFRACTION99
2.38-2.490.22041500.16782636X-RAY DIFFRACTION99
2.49-2.620.20291400.17842635X-RAY DIFFRACTION100
2.62-2.780.21241410.17992640X-RAY DIFFRACTION100
2.78-30.2171490.18662645X-RAY DIFFRACTION100
3-3.30.21561500.18042673X-RAY DIFFRACTION100
3.3-3.770.18111440.16062658X-RAY DIFFRACTION100
3.77-4.750.16161580.13472665X-RAY DIFFRACTION100
4.75-33.170.17031870.15552671X-RAY DIFFRACTION99

+
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