[English] 日本語
Yorodumi
- PDB-7zkj: CODH/ACS complex of C. hydrogenoformans -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zkj
TitleCODH/ACS complex of C. hydrogenoformans
Components
  • CO-methylating acetyl-CoA synthase
  • Carbon monoxide dehydrogenase
KeywordsOXIDOREDUCTASE / CO2 reduction / acetyl-CoA synthesis / carbon monoxide
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
Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3 / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3 / 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 ...Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3 / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3 / 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 / 2-Layer Sandwich / Alpha Beta
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: 2.04 Å
AuthorsRuickoldt, J. / Jeoung, J.-H. / Basak, Y. / Domnik, L. / Dobbek, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)EXC 2008/1 390540038 Germany
CitationJournal: ACS Catal. / Year: 2022
Title: On the Kinetics of CO2 Reduction by Ni, Fe-CO Dehydrogenases
Authors: Ruickoldt, J. / Basak, Y. / Domnik, L. / Jeoung, J.H. / Dobbek, H.
History
DepositionApr 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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
B: CO-methylating acetyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,39517
Polymers155,2832
Non-polymers2,11215
Water15,907883
1
B: CO-methylating acetyl-CoA synthase
hetero molecules

B: CO-methylating acetyl-CoA synthase
hetero molecules

A: Carbon monoxide dehydrogenase
hetero molecules

A: Carbon monoxide dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,79134
Polymers310,5674
Non-polymers4,22430
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
crystal symmetry operation6_555x-y,x,z+1/61
crystal symmetry operation8_545x-y,-y-1,-z1
Buried area23280 Å2
ΔGint-314 kcal/mol
Surface area88330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.586, 141.586, 290.124
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-1075-

HOH

21A-1170-

HOH

31B-931-

HOH

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Carbon monoxide dehydrogenase


Mass: 73172.102 Da / Num. of mol.: 1
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: 82111.172 Da / Num. of mol.: 1
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: acsB, CHY_1222 / Production host: Escherichia coli (E. coli)
References: UniProt: Q3ACS4, CO-methylating acetyl-CoA synthase

-
Non-polymers , 9 types, 898 molecules

#3: 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
#4: 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
#5: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO
#6: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#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: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#10: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 883 / 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: 2.7 Å3/Da / Density % sol: 54.5 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 4.85
Details: 0.7 uL of the reservoir solution (0.1 M sodium acetate, 210 g/L MPD, 60 g/L PEG 4000) were mixed with 0.7 uL 19.6 g/L CODH/ACS in 50 mM Mops pH 7.6, 150 mM NaCl, 1.6 mM Ti(III)-EDTA to form ...Details: 0.7 uL of the reservoir solution (0.1 M sodium acetate, 210 g/L MPD, 60 g/L PEG 4000) were mixed with 0.7 uL 19.6 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 S 6M / Detector: PIXEL / Date: Oct 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.93→48.35 Å / Num. obs: 129067 / % possible obs: 99.84 % / Redundancy: 19.8 % / CC1/2: 0.999 / Net I/σ(I): 10.2
Reflection shellResolution: 1.93→2 Å / Num. unique obs: 12539 / CC1/2: 0.316 / % possible all: 98.55

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1aoa

1aoa


Resolution: 2.04→48.35 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1987 2181 1.05 %
Rwork0.1744 204863 -
obs0.1746 109315 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.84 Å2 / Biso mean: 41.2908 Å2 / Biso min: 20.51 Å2
Refinement stepCycle: final / Resolution: 2.04→48.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10906 0 66 883 11855
Biso mean--48.81 45.54 -
Num. residues----1399
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.04-2.080.35981340.32931284712981
2.08-2.130.33721390.30581276712906
2.13-2.190.3531350.28411279112926
2.19-2.250.2881390.26391283312972
2.25-2.310.26011360.25511276212898
2.31-2.390.27621370.22581283012967
2.39-2.470.2631340.21931277212906
2.47-2.570.25821350.20771281012945
2.57-2.690.28021330.19311281912952
2.69-2.830.17251400.17681282312963
2.83-3.010.21641350.17321275712892
3.01-3.240.20641340.15751281012944
3.24-3.560.15241360.14951281812954
3.56-4.080.15081360.1311282912965
4.08-5.140.14061360.12781280612942
5.14-48.350.17051420.1571278912931
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)
10.61330.0895-0.2860.7912-0.11631.0267-0.0199-0.1121-0.02530.1335-0.0406-0.2117-0.00660.36760.06080.2708-0.00120.0010.35990.07310.3217-34.3361-48.6463-23.849
21.08480.4037-0.22691.16070.5162.13570.0420.09310.2740.024-0.05010.2865-0.324-0.25470.01980.25890.02510.02530.25750.07210.3318-57.538-34.7487-27.7955
31.63280.3913-0.23091.7481-0.86431.15680.0695-0.40520.04640.3634-0.0767-0.0197-0.18840.27280.00750.4561-0.02220.0020.41880.00010.3118-41.8023-34.0971-1.7494
40.96620.032-0.39251.22260.49262.14080.0488-0.13490.15860.1622-0.0377-0.1198-0.2350.2963-0.01350.2363-0.03780.00570.28690.0430.2976-35.1287-27.1382-30.659
50.6705-0.05770.09391.1979-0.16231.5442-0.02990.10530.029-0.10520.0285-0.03010.02370.1174-0.00180.224-0.037-0.02420.23730.01720.220317.6328-57.7576-14.8478
64.7047-1.62271.29891.049-0.71411.25880.05010.40180.3773-0.0179-0.1201-0.1687-0.26060.09890.08230.3964-0.0814-0.01510.41170.04690.321616.4294-39.3459-22.4969
71.5808-0.28820.00191.67410.60171.982-0.03340.28410.2182-0.21720.0037-0.0535-0.2437-0.06520.02110.369-0.0359-0.03810.41320.11890.3465-0.8403-32.3173-43.2414
81.39390.5268-0.26462.208-0.2092.0019-0.05630.16950.0193-0.30180.0519-0.2685-0.01520.19910.00280.2789-0.03790.0180.25670.00450.24499.1774-62.6951-49.3022
93.17510.8113-0.1651.29580.37941.88690.02710.11850.11910.0567-0.03230.167-0.028-0.17250.00320.3116-0.02380.00920.23840.01530.2622-8.2029-68.2601-40.7316
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 128 )A2 - 128
2X-RAY DIFFRACTION2chain 'A' and (resid 129 through 255 )A129 - 255
3X-RAY DIFFRACTION3chain 'A' and (resid 256 through 410 )A256 - 410
4X-RAY DIFFRACTION4chain 'A' and (resid 411 through 670 )A411 - 670
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 286 )B5 - 286
6X-RAY DIFFRACTION6chain 'B' and (resid 287 through 346 )B287 - 346
7X-RAY DIFFRACTION7chain 'B' and (resid 347 through 497 )B347 - 497
8X-RAY DIFFRACTION8chain 'B' and (resid 498 through 618 )B498 - 618
9X-RAY DIFFRACTION9chain 'B' and (resid 619 through 734 )B619 - 734

+
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