[English] 日本語
Yorodumi
- PDB-8cja: A225L/F231A variant of the CODH/ACS complex of C. hydrogenoformans -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8cja
TitleA225L/F231A variant of the CODH/ACS complex of C. hydrogenoformans
Components
  • CO-methylating acetyl-CoA synthase
  • Carbon monoxide dehydrogenase
KeywordsOXIDOREDUCTASE / CODH / ACS
Function / homology
Function and homology information


CO-methylating acetyl-CoA synthase / CO-methylating acetyl-CoA synthase activity / anaerobic carbon monoxide dehydrogenase / hydroxylamine reductase activity / anaerobic carbon-monoxide dehydrogenase activity / acetyl-CoA metabolic process / nickel cation binding / generation of precursor metabolites and energy / peroxidase activity / response to hydrogen peroxide ...CO-methylating acetyl-CoA synthase / CO-methylating acetyl-CoA synthase activity / anaerobic carbon monoxide dehydrogenase / hydroxylamine reductase activity / anaerobic carbon-monoxide dehydrogenase activity / acetyl-CoA metabolic process / 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 / metal ion binding
Similarity search - Function
Carbon monoxide dehydrogenase subunit alpha ,N-terminal / Carbon monoxide dehydrogenase subunit alpha N-terminal domain / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase, domain 3 superfamily / CO dehydrogenase/acetyl-CoA synthase complex beta subunit , C-terminal / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / ACS/CODH beta subunit C-terminal / Ni-containing CO dehydrogenase / CO dehydrogenase, alpha-bundle / Hydroxylamine reductase/Ni-containing CO dehydrogenase ...Carbon monoxide dehydrogenase subunit alpha ,N-terminal / Carbon monoxide dehydrogenase subunit alpha N-terminal domain / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase, domain 3 superfamily / CO dehydrogenase/acetyl-CoA synthase complex beta subunit , C-terminal / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / ACS/CODH beta subunit C-terminal / 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
ACETATE ION / NICKEL (II) ION / HYDROXIDE ION / Fe(3)-Ni(1)-S(4) cluster / IRON/SULFUR CLUSTER / Carbon monoxide dehydrogenase / CO-methylating acetyl-CoA synthase
Similarity search - Component
Biological speciesCarboxydothermus hydrogenoformans Z-2901 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRuickoldt, J. / Jeoung, J. / Lennartz, F. / Dobbek, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)EXC 2008 390540038 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Coupling CO 2 Reduction and Acetyl-CoA Formation: The Role of a CO Capturing Tunnel in Enzymatic Catalysis.
Authors: Ruickoldt, J. / Jeoung, J.H. / Rudolph, M.A. / Lennartz, F. / Kreibich, J. / Schomacker, R. / Dobbek, H.
History
DepositionFeb 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carbon monoxide dehydrogenase
B: CO-methylating acetyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,25313
Polymers156,3412
Non-polymers1,91211
Water13,385743
1
A: Carbon monoxide dehydrogenase
B: CO-methylating acetyl-CoA synthase
hetero molecules

A: Carbon monoxide dehydrogenase
B: CO-methylating acetyl-CoA synthase
hetero molecules

B: CO-methylating acetyl-CoA synthase
hetero molecules

B: CO-methylating acetyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)484,05036
Polymers479,1706
Non-polymers4,88030
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
crystal symmetry operation5_554y,-x+y,z-1/61
crystal symmetry operation8_445x-y-1,-y-1,-z1
Buried area22120 Å2
ΔGint-322 kcal/mol
Surface area89520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.219, 142.219, 290.773
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-944-

HOH

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Carbon monoxide dehydrogenase


Mass: 73096.000 Da / Num. of mol.: 1 / Mutation: F231A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans Z-2901 (bacteria)
Gene: ciss_06270 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1L8D0M5, anaerobic carbon monoxide dehydrogenase
#2: Protein CO-methylating acetyl-CoA synthase


Mass: 83244.516 Da / Num. of mol.: 1 / Mutation: A225L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans Z-2901 (bacteria)
Gene: acsB, CHY_1222 / Production host: Escherichia coli (E. coli)
References: UniProt: Q3ACS4, CO-methylating acetyl-CoA synthase

-
Non-polymers , 7 types, 754 molecules

#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-RQM / Fe(3)-Ni(1)-S(4) cluster


Mass: 410.333 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4NiS4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 743 / 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: 2.71 Å3/Da / Density % sol: 54.54 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 1.12 uL of the reservoir solution (0.1 M sodium acetate, 250 g/L MPD, 40 g/L PEG 4000) were mixed with 0.28 uL 23.7 g/L CODH/ACS in 50 mM Mops pH 7.6, 150 mM NaCl, 1.6 mM Ti(III)-EDTA to ...Details: 1.12 uL of the reservoir solution (0.1 M sodium acetate, 250 g/L MPD, 40 g/L PEG 4000) were mixed with 0.28 uL 23.7 g/L CODH/ACS in 50 mM Mops pH 7.6, 150 mM NaCl, 1.6 mM Ti(III)-EDTA to form the sitting drop. Crystallization was performed in an anoxic glove box.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.91→48.46 Å / Num. obs: 134637 / % possible obs: 99.89 % / Redundancy: 19.8 % / CC1/2: 0.998 / Rpim(I) all: 0.071 / Net I/σ(I): 9.4
Reflection shellResolution: 1.91→1.98 Å / Redundancy: 19.15 % / Num. unique obs: 13158 / CC1/2: 0.205 / % possible all: 99.06

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→46.55 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.31 / Phase error: 23.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2092 1993 1.04 %Random selection
Rwork0.178 ---
obs0.1783 101450 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→46.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10946 0 20 743 11709
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911268
X-RAY DIFFRACTIONf_angle_d1.07515284
X-RAY DIFFRACTIONf_dihedral_angle_d8.5231540
X-RAY DIFFRACTIONf_chiral_restr0.071695
X-RAY DIFFRACTIONf_plane_restr0.0091983
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.31891440.320913606X-RAY DIFFRACTION100
2.15-2.210.34081400.298613501X-RAY DIFFRACTION100
2.21-2.280.28751450.275413565X-RAY DIFFRACTION100
2.28-2.350.28651410.258613588X-RAY DIFFRACTION100
2.35-2.430.29971390.24213539X-RAY DIFFRACTION100
2.43-2.530.28681430.23413614X-RAY DIFFRACTION100
2.53-2.650.22521400.21413560X-RAY DIFFRACTION100
2.65-2.790.21651420.200913575X-RAY DIFFRACTION100
2.79-2.960.2291470.186913570X-RAY DIFFRACTION100
2.96-3.190.21351400.180313545X-RAY DIFFRACTION100
3.19-3.510.19351380.16113579X-RAY DIFFRACTION100
3.51-4.020.15481470.14113539X-RAY DIFFRACTION100
4.02-5.060.16171440.127813600X-RAY DIFFRACTION100
5.06-46.550.19011430.150713539X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5050.0628-0.20660.7288-0.18010.8408-0.0354-0.06980.00670.0803-0.04-0.1970.01740.35170.03960.29080.02990.01290.42850.08910.3655-34.2202-49.0482-24.0468
20.81610.3044-0.20491.40190.53842.10490.04670.07550.2477-0.0157-0.09250.3101-0.3009-0.26780.07520.26470.04470.0210.31390.07380.3736-57.955-34.8461-27.6266
32.394-0.00340.20981.5352-1.45052.04520.0586-0.53520.22570.4837-0.0966-0.021-0.46640.12570.03470.5318-0.04220.03140.4615-0.03160.3973-41.8569-27.0977-1.2226
42.9002-0.3334-0.38021.31860.64521.0634-0.0133-0.2111-0.19650.2152-0.0518-0.0444-0.05460.4570.07190.4912-0.0223-0.00210.53220.05130.3748-37.7502-36.9297-4.9178
50.66290.0002-0.46920.788-0.03752.00770.0424-0.15690.0990.172-0.0527-0.0711-0.19340.31090.00650.2533-0.0177-0.00480.33570.05120.3347-37.1454-28.9722-26.2666
60.66630.09590.09511.1387-0.14831.4299-0.03930.09780.034-0.0920.035-0.06610.0120.2156-0.00130.246-0.0423-0.03340.2730.02580.240517.6899-58.0939-14.918
75.9651-2.19371.9941.3707-0.8931.7181-0.05540.38170.45670.0187-0.1273-0.2524-0.31750.16310.20710.404-0.1193-0.01520.41790.06870.341516.1449-39.5311-22.741
82.0157-0.5997-0.22142.1510.70752.8955-0.00960.28060.2428-0.18940.0311-0.0843-0.3054-0.1235-0.01380.3196-0.0405-0.03150.37370.12790.3338-0.8504-32.5874-43.3449
93.1361.5525-1.16592.2557-0.55312.3793-0.0420.16090.0289-0.11770.0451-0.0039-0.0083-0.03080.00310.28690.0014-0.01270.21080.00910.21890.9805-65.7862-45.3067
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 127 )
2X-RAY DIFFRACTION2chain 'A' and (resid 128 through 255 )
3X-RAY DIFFRACTION3chain 'A' and (resid 256 through 308 )
4X-RAY DIFFRACTION4chain 'A' and (resid 309 through 371 )
5X-RAY DIFFRACTION5chain 'A' and (resid 372 through 670 )
6X-RAY DIFFRACTION6chain 'B' and (resid 5 through 286 )
7X-RAY DIFFRACTION7chain 'B' and (resid 287 through 346 )
8X-RAY DIFFRACTION8chain 'B' and (resid 347 through 497 )
9X-RAY DIFFRACTION9chain 'B' and (resid 498 through 735 )

+
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