[English] 日本語
Yorodumi
- PDB-6x5k: Crystal structure of CODH/ACS with carbon monoxide bound to the A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6x5k
TitleCrystal structure of CODH/ACS with carbon monoxide bound to the A-cluster
Components(Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit ...) x 2
KeywordsOXIDOREDUCTASE/TRANSFERASE / CODH / ACS / carbon monoxide dehydrogenase / acetyl-CoA synthase / OXIDOREDUCTASE / OXIDOREDUCTASE-TRANSFERASE complex
Function / homology
Function and homology information


CO-methylating acetyl-CoA synthase / CO-methylating acetyl-CoA synthase activity / anaerobic carbon monoxide dehydrogenase / carbon-monoxide dehydrogenase (ferredoxin) activity / carbon-monoxide dehydrogenase (acceptor) activity / acetyl-CoA metabolic process / carbon fixation / nickel cation binding / generation of precursor metabolites and energy / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
CO dehydrogenase/acetyl-CoA synthase complex beta subunit , C-terminal / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase, domain 3 superfamily / Carbon monoxide dehydrogenase subunit alpha ,N-terminal / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / Carbon monoxide dehydrogenase subunit alpha N-terminal domain / ACS/CODH beta subunit C-terminal / Ni-containing CO dehydrogenase / CO dehydrogenase, alpha-bundle / Hydroxylamine reductase/Ni-containing CO dehydrogenase ...CO dehydrogenase/acetyl-CoA synthase complex beta subunit , C-terminal / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase, domain 3 superfamily / Carbon monoxide dehydrogenase subunit alpha ,N-terminal / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / Carbon monoxide dehydrogenase subunit alpha N-terminal domain / 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
CARBON MONOXIDE / NICKEL (II) ION / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / TRIETHYLENE GLYCOL / IRON/SULFUR CLUSTER / FE(4)-NI(1)-S(4) CLUSTER / Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha / Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit beta
Similarity search - Component
Biological speciesMoorella thermoacetica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsCohen, S.E. / Wittenborn, E.C. / Hendrickson, R. / Drennan, C.L.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM126982 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM008334 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124165 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: Acs Catalysis / Year: 2020
Title: Crystallographic Characterization of the Carbonylated A-Cluster in Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase
Authors: Cohen, S.E. / Can, M. / Wittenborn, E.C. / Hendrickson, R.A. / Ragsdale, S.W. / Drennan, C.L.
History
DepositionMay 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit beta
B: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit beta
C: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit beta
D: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit beta
M: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha
N: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha
O: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha
P: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)625,35936
Polymers619,2958
Non-polymers6,06428
Water8,431468
1
A: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit beta
B: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit beta
M: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha
N: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)312,69219
Polymers309,6484
Non-polymers3,04415
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21310 Å2
ΔGint-294 kcal/mol
Surface area87900 Å2
MethodPISA
2
C: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit beta
D: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit beta
O: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha
P: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)312,66817
Polymers309,6484
Non-polymers3,02013
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20810 Å2
ΔGint-277 kcal/mol
Surface area89010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.729, 137.383, 141.867
Angle α, β, γ (deg.)101.818, 109.077, 103.657
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

-
Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit ... , 2 types, 8 molecules ABCDMNOP

#1: Protein
Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit beta / Carbon monoxide dehydrogenase subunit


Mass: 73006.930 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Moorella thermoacetica (bacteria)
References: UniProt: P27989, anaerobic carbon monoxide dehydrogenase
#2: Protein
Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha / CODH/ACS


Mass: 81816.930 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Moorella thermoacetica (bacteria)
References: UniProt: P27988, CO-methylating acetyl-CoA synthase

-
Non-polymers , 8 types, 496 molecules

#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-XCC / FE(4)-NI(1)-S(4) CLUSTER / C CLUSTER


Mass: 410.333 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4NiS4
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / Triethylene glycol dimethyl ether


Mass: 178.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O4
#7: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-CMO / CARBON MONOXIDE / Carbon monoxide


Mass: 28.010 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CO / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 468 / 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: 2.74 Å3/Da / Density % sol: 55.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: PIPES, pH 6.5; magnesium acetate, glycerol, sodium dithionite, dithiothreitol, PEG 8000, sodium dodecanoyl sarcosine

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.47→49.63 Å / Num. obs: 204543 / % possible obs: 88.3 % / Redundancy: 7.2 % / Biso Wilson estimate: 39.81 Å2 / CC1/2: 0.99 / Net I/σ(I): 9.6
Reflection shellResolution: 2.47→2.57 Å / Num. unique obs: 14748 / CC1/2: 0.8

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1mjg

1mjg


Resolution: 2.47→49.63 Å / SU ML: 0.3274 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.199
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2336 10236 5 %
Rwork0.2034 194307 -
obs0.2049 204543 86.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52 Å2
Refinement stepCycle: LAST / Resolution: 2.47→49.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms43301 0 143 468 43912
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001744480
X-RAY DIFFRACTIONf_angle_d0.496660372
X-RAY DIFFRACTIONf_chiral_restr0.04026684
X-RAY DIFFRACTIONf_plane_restr0.00227843
X-RAY DIFFRACTIONf_dihedral_angle_d16.905716615
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.47-2.50.34741580.3112904X-RAY DIFFRACTION38.74
2.5-2.530.32042490.30764616X-RAY DIFFRACTION61.9
2.53-2.560.34682520.29814679X-RAY DIFFRACTION63.1
2.56-2.590.33512760.2985289X-RAY DIFFRACTION71.37
2.59-2.630.33173270.28996058X-RAY DIFFRACTION80.61
2.63-2.660.32313210.29546234X-RAY DIFFRACTION84.4
2.66-2.70.32133450.28886554X-RAY DIFFRACTION87.86
2.7-2.740.34243560.28446792X-RAY DIFFRACTION91.01
2.74-2.790.31653660.27836924X-RAY DIFFRACTION92.4
2.79-2.830.3023670.27166911X-RAY DIFFRACTION92.9
2.83-2.880.32183630.26676894X-RAY DIFFRACTION92.82
2.88-2.930.28783790.25546897X-RAY DIFFRACTION92.31
2.93-2.990.29093250.25036775X-RAY DIFFRACTION91.13
2.99-3.050.30353690.24766720X-RAY DIFFRACTION90.05
3.05-3.120.29713430.23666418X-RAY DIFFRACTION86.13
3.12-3.190.27113470.22686492X-RAY DIFFRACTION87.54
3.19-3.270.24273740.21927035X-RAY DIFFRACTION94.96
3.27-3.360.24153570.21997106X-RAY DIFFRACTION95.08
3.36-3.460.23993970.20677063X-RAY DIFFRACTION94.92
3.46-3.570.21173330.1897066X-RAY DIFFRACTION94.38
3.57-3.690.21413820.18746963X-RAY DIFFRACTION93.46
3.69-3.840.2113660.17886878X-RAY DIFFRACTION92.34
3.84-4.020.19153500.17946697X-RAY DIFFRACTION90.2
4.02-4.230.19713260.16936465X-RAY DIFFRACTION86.99
4.23-4.490.19413810.15757164X-RAY DIFFRACTION95.98
4.49-4.840.19683820.16227105X-RAY DIFFRACTION95.44
4.84-5.330.19593700.16937006X-RAY DIFFRACTION94.11
5.33-6.10.20733360.18236577X-RAY DIFFRACTION88.19
6.1-7.680.21083820.17547124X-RAY DIFFRACTION95.56
7.68-49.630.16983570.16366901X-RAY DIFFRACTION92.67
Refinement TLS params.Method: refined / Origin x: 11.6167974868 Å / Origin y: 84.3987016688 Å / Origin z: 83.0510552734 Å
111213212223313233
T0.166759428175 Å2-0.0136611053074 Å20.0259861517333 Å2-0.166198055656 Å20.00511694574454 Å2--0.162439469687 Å2
L0.104947071894 °2-0.01554439528 °20.0855868823108 °2-0.0332638602031 °2-0.0275370417512 °2--0.0981948255985 °2
S-0.0236558923392 Å °-0.039222284351 Å °0.00834361310431 Å °0.00503456920237 Å °0.00821796689999 Å °0.0217524510079 Å °-0.0368942626585 Å °-0.032638266394 Å °-0.000284272882683 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