[English] 日本語
Yorodumi
- PDB-7err: Tunnel-redesigned O2-tolerant CO dehydrogenase for removal of CO ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7err
TitleTunnel-redesigned O2-tolerant CO dehydrogenase for removal of CO in real flue gas (Aerobic ChCODH2 A559W mutant)
ComponentsCarbon monoxide dehydrogenase 2
KeywordsOXIDOREDUCTASE / Carbon monoxide dehydrogenase / ELECTRON TRANSPORT
Function / homology
Function and homology information


anaerobic carbon monoxide dehydrogenase / anaerobic carbon-monoxide dehydrogenase activity / hydroxylamine reductase 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 / FE(4)-NI(1)-S(5) CLUSTER / IRON/SULFUR CLUSTER / Carbon monoxide dehydrogenase 2
Similarity search - Component
Biological speciesCarboxydothermus hydrogenoformans Z-2901 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsHeo, Y.Y. / Kim, S.M.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2015M3D3A1A01064919 Korea, Republic Of
National Research Foundation (NRF, Korea)2020R1A5A1019631 Korea, Republic Of
CitationJournal: Nat Catal / Year: 2022
Title: O2-tolerant CO dehydrogenase via tunnel redesign for the removal of CO from industrial flue gas
Authors: Kim, S.M. / Lee, J.H. / Kang, S.H. / Heo, Y.Y. / Yoon, H.J. / Hahn, J.S. / Lee, H.H. / Kim, Y.H.
History
DepositionMay 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: 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.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
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)70,2774
Polymers69,3071
Non-polymers9703
Water4,071226
1
A: Carbon monoxide dehydrogenase 2
hetero molecules

A: Carbon monoxide dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,5548
Polymers138,6142
Non-polymers1,9406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8480 Å2
ΔGint-120 kcal/mol
Surface area37400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.144, 75.137, 70.785
Angle α, β, γ (deg.)90.000, 111.200, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Carbon monoxide dehydrogenase 2 / CODH 2


Mass: 69307.023 Da / Num. of mol.: 1 / Mutation: A559W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans Z-2901 (bacteria)
Strain: ATCC BAA-161 / DSM 6008 / Z-2901 / Gene: cooS2, cooSII, CHY_0085 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9F8A8, anaerobic carbon monoxide dehydrogenase
#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-NFS / FE(4)-NI(1)-S(5) CLUSTER


Mass: 442.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4NiS5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
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: 38.68 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M HEPES/NaOH pH 7.0, 50 mM MgCl2, 25 % (w/v) polyethyleneglycol 3350

-
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: Oct 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. obs: 25635 / % possible obs: 99.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 32.26 Å2 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.063 / Rrim(I) all: 0.118 / Χ2: 0.681 / Net I/σ(I): 5.5 / Num. measured all: 86418
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.26-2.33.10.51312130.8060.3310.6120.595.2
2.3-2.343.20.4912830.8150.3180.5860.49697.8
2.34-2.393.20.41912350.880.2710.5010.49998.7
2.39-2.433.30.41912870.8370.2680.4980.49599.8
2.43-2.493.30.35412830.8910.2280.4220.47599.6
2.49-2.553.30.32812740.910.2140.3930.599.8
2.55-2.6130.2812860.9130.1940.3420.486100
2.61-2.683.20.25312800.9230.1690.3050.5299.9
2.68-2.763.20.22712610.9340.1490.2730.51499.9
2.76-2.853.40.20512970.9550.1290.2420.527100
2.85-2.953.60.18913010.9660.1140.2210.54799.8
2.95-3.073.60.14712800.9830.0890.1720.545100
3.07-3.213.60.12712880.9830.0780.1490.597100
3.21-3.383.60.10412970.9880.0640.1220.62599.9
3.38-3.593.60.08312760.9920.0510.0980.71999.8
3.59-3.863.50.06612790.9940.0410.0780.78999.8
3.86-4.253.50.05512870.9950.0340.0650.97599.5
4.25-4.873.10.05112990.9940.0340.0611.09799.5
4.87-6.133.30.0513040.9940.0330.061.01899.8
6.13-503.70.04413250.9970.0270.0521.51799.5

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SU7

1su7


Resolution: 2.26→40.72 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 17.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1976 1235 4.82 %RANDOM
Rwork0.1443 24397 --
obs0.1468 25632 99.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.07 Å2 / Biso mean: 35.9194 Å2 / Biso min: 17.7 Å2
Refinement stepCycle: final / Resolution: 2.26→40.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4619 0 22 226 4867
Biso mean--48.1 38.07 -
Num. residues----633
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.26-2.350.21941410.1492603274496
2.35-2.460.21491420.13932667280999
2.46-2.590.23261210.132327522873100
2.59-2.750.20361320.137827002832100
2.75-2.960.22391230.154527302853100
2.96-3.260.20881330.159127302863100
3.26-3.730.18491670.145427092876100
3.73-4.70.17391320.12927282860100
4.7-40.720.19391440.15227782922100

+
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