[English] 日本語
Yorodumi
- PDB-8x9f: Crystal structure of CO dehydrogenase mutant in complex with EV -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8x9f
TitleCrystal structure of CO dehydrogenase mutant in complex with EV
ComponentsCarbon monoxide dehydrogenase 2
KeywordsELECTRON TRANSPORT / OXIDOREDUCTASE
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: 2.48 Å
AuthorsLee, H.H. / Heo, Y. / Yoon, H.J. / Kim, S.M. / Kong, S.Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Other government Korea, Republic Of
CitationJournal: Nat Commun / Year: 2024
Title: Identifying a key spot for electron mediator-interaction to tailor CO dehydrogenase's affinity.
Authors: Kim, S.M. / Kang, S.H. / Lee, J. / Heo, Y. / Poloniataki, E.G. / Kang, J. / Yoon, H.J. / Kong, S.Y. / Yun, Y. / Kim, H. / Ryu, J. / Lee, H.H. / Kim, Y.H.
History
DepositionNov 30, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

-
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)70,2776
Polymers69,0631
Non-polymers1,2145
Water2,108117
1
A: Carbon monoxide dehydrogenase 2
hetero molecules

A: Carbon monoxide dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,55412
Polymers138,1262
Non-polymers2,42810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
MethodPISA
Unit cell
Length a, b, c (Å)112.251, 74.783, 71.214
Angle α, β, γ (deg.)90.00, 111.18, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-705-

EDO

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Carbon monoxide dehydrogenase 2 / CODH 2


Mass: 69062.789 Da / Num. of mol.: 1 / Mutation: R57G, N59L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans Z-2901 (bacteria)
Strain: Z-2901 / Gene: cooS2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9F8A8, anaerobic carbon monoxide dehydrogenase

-
Non-polymers , 6 types, 122 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-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-S8I / 1-ethyl-4-(1-ethylpyridin-1-ium-4-yl)pyridin-1-ium


Mass: 214.306 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H18N2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.01 Å3/Da / Density % sol: 38.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES/NaOH pH 7.5, 200 mM MgCl2, and 25% (w/v) polyethylene glycol 3,350

-
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 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.48→30 Å / Num. obs: 19005 / % possible obs: 98 % / Redundancy: 3.6 % / CC1/2: 0.986 / CC star: 0.997 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.069 / Rrim(I) all: 0.134 / Χ2: 0.537 / Net I/σ(I): 4.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.5-2.543.70.4399090.8090.9460.2640.5140.41498.9
2.54-2.593.60.3969660.8190.9490.2410.4660.43298.8
2.59-2.643.40.3459420.8350.9540.2240.4140.45599.1
2.64-2.693.30.3199690.8080.9450.2080.3830.48798.8
2.69-2.753.50.2959580.8770.9670.1850.350.47698.9
2.75-2.823.80.2679550.9170.9780.1590.3120.42898.8
2.82-2.894.10.2589510.930.9820.1440.2960.4399
2.89-2.9640.2449570.9340.9830.1390.2820.43798.7
2.96-3.0540.2029520.9620.990.1140.2330.47798.4
3.05-3.153.90.189460.9680.9920.1030.2070.4698.2
3.15-3.263.90.1549450.9760.9940.0880.1780.50698
3.26-3.393.80.1419540.9770.9940.0820.1640.51998.4
3.39-3.553.70.1219380.9780.9950.0710.1410.61597.4
3.55-3.733.70.1069410.9810.9950.0630.1240.66897
3.73-3.973.50.0949560.9820.9950.0570.1110.70497.3
3.97-4.273.40.0689210.990.9970.0420.080.60696
4.27-4.73.10.0639260.9910.9980.0410.0760.59194.9
4.7-5.382.90.0559480.9920.9980.0390.0680.57396.7
5.38-6.763.80.069780.9940.9990.0350.0690.51598.9
6.76-303.70.0539930.9940.9990.0310.0610.99798.9

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→28.05 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2673 943 5 %
Rwork0.2446 --
obs0.2457 18865 96.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.48→28.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4687 0 0 117 4804
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034765
X-RAY DIFFRACTIONf_angle_d0.6286483
X-RAY DIFFRACTIONf_dihedral_angle_d6.373668
X-RAY DIFFRACTIONf_chiral_restr0.045778
X-RAY DIFFRACTIONf_plane_restr0.006834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.610.30141210.30372422X-RAY DIFFRACTION92
2.61-2.780.28641390.29562557X-RAY DIFFRACTION98
2.78-2.990.26581300.28222590X-RAY DIFFRACTION98
2.99-3.290.271530.2692567X-RAY DIFFRACTION97
3.29-3.770.27991380.24182575X-RAY DIFFRACTION97
3.77-4.740.24191350.21262551X-RAY DIFFRACTION96
4.74-28.050.26371270.21452660X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 13.9311 Å / Origin y: -0.6029 Å / Origin z: 14.486 Å
111213212223313233
T0.2049 Å2-0.0043 Å20.0041 Å2-0.2008 Å20.0082 Å2--0.1959 Å2
L0.5579 °20.0023 °20.078 °2-0.4853 °20.0257 °2--0.4149 °2
S-0.0194 Å °-0.1094 Å °-0.0503 Å °0.1173 Å °-0.005 Å °-0.0177 Å °-0.0549 Å °-0.0135 Å °0.0133 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