[English] 日本語
Yorodumi
- PDB-9g7j: Crystal structure of the tungsten-dependent aldehyde:ferredoxin o... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9g7j
TitleCrystal structure of the tungsten-dependent aldehyde:ferredoxin oxidoreductase from Clostridium autoethanogenum.
ComponentsAldehyde ferredoxin oxidoreductase
KeywordsOXIDOREDUCTASE / Anaerobic metabolism / Metalloenzyme / Tungstopterin / Ethanol production / acetogenic bacteria / iron-sulfur cluster
Function / homology
Function and homology information


oxidoreductase activity, acting on the aldehyde or oxo group of donors, iron-sulfur protein as acceptor / 4 iron, 4 sulfur cluster binding / electron transfer activity / metal ion binding
Similarity search - Function
Aldehyde ferredoxin oxidoreductase, C-terminal / Aldehyde ferredoxin oxidoreductase, N-terminal / Aldehyde ferredoxin oxidoreductase, domain 2 / Aldehyde ferredoxin oxidoreductase, domain 3 / Aldehyde ferredoxin oxidoreductase-like, C-terminal / Aldehyde ferredoxin oxidoreductase, N-terminal domain superfamily / : / Aldehyde ferredoxin oxidoreductase, domains 2 & 3 / Aldehyde ferredoxin oxidoreductase, N-terminal domain / Aldehyde ferredoxin oxidoreductase, N-terminal domain
Similarity search - Domain/homology
: / IRON/SULFUR CLUSTER / Aldehyde ferredoxin oxidoreductase
Similarity search - Component
Biological speciesClostridium autoethanogenum DSM 10061 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.59 Å
AuthorsLemaire, O.N. / Wagner, T.
Funding support Germany, 2items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)DFG-SPP 1927 WA 4053/1-1 Germany
CitationJournal: Nat.Chem.Biol. / Year: 2025
Title: Carbon-monoxide-driven bioethanol production operates through a tungsten-dependent catalyst.
Authors: Lemaire, O.N. / Belhamri, M. / Shevchenko, A. / Wagner, T.
History
DepositionJul 21, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2025Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aldehyde ferredoxin oxidoreductase
B: Aldehyde ferredoxin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,76712
Polymers132,8232
Non-polymers2,94410
Water27,0951504
1
A: Aldehyde ferredoxin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8165
Polymers66,4121
Non-polymers1,4044
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aldehyde ferredoxin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9517
Polymers66,4121
Non-polymers1,5396
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.595, 100.436, 176.595
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-1378-

HOH

21A-1399-

HOH

31A-1444-

HOH

41A-1581-

HOH

51B-1470-

HOH

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Aldehyde ferredoxin oxidoreductase / Oxidoreductase YdhV


Mass: 66411.727 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Monomeric metalloenzyme containing an [4Fe-4S] cluster, a tungsten-dependent bis-pyranopterin cofacor and a Mg ion.
Source: (natural) Clostridium autoethanogenum DSM 10061 (bacteria)
Cell line: / / Organ: / / Plasmid details: / / Variant: wild type / Strain: DSM 10061 / Tissue: / / References: UniProt: A0A3M0S906, Oxidoreductases

-
Non-polymers , 6 types, 1514 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1IJH / Tungstopterin cofactor


Mass: 992.801 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H22MgN10O12P2S4W / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1504 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.06 % / Description: Irregular polygonal brown crystal.
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Crystals were obtained by initial screening at 20 degrees Celsius using the sitting drop method on a 96-Well MRC 2-Drop Crystallization Plates in polystyrene (SWISSCI). The crystallization ...Details: Crystals were obtained by initial screening at 20 degrees Celsius using the sitting drop method on a 96-Well MRC 2-Drop Crystallization Plates in polystyrene (SWISSCI). The crystallization reservoir contained 90 ul of mother liquor, the crystallization drop contained a mixture of 0.55 ul protein at 8.6 mg.ml-1 and 0.55 ul precipitant. The protein was in 25 mM Tris/HCl buffer pH 7.6, 10 % (v/v) glycerol, and 2 mM dithiothreitol. The crystal was obtained in a Coy tent under an N2/H2 atmosphere (96:4 %). The crystallization reservoir contained 25% (w/v) PEG 3350, 100 mM BIS-Tris pH 6.5, 200 mM Magnesium chloride hexahydrate. The crystal was soaked in the crystallization solution supplemented with 25 % (v/v) glycerol before freezing in liquid nitrogen.
PH range: / / Temp details: /

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.21434 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.21434 Å / Relative weight: 1
ReflectionResolution: 1.59→100.44 Å / Num. obs: 116033 / % possible obs: 95.1 % / Redundancy: 12.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.072 / Rrim(I) all: 0.187 / Net I/σ(I): 8.4
Reflection shellResolution: 1.595→1.736 Å / Redundancy: 12.2 % / Rmerge(I) obs: 1.725 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 5802 / CC1/2: 0.641 / Rpim(I) all: 0.746 / Rrim(I) all: 1.882 / % possible all: 63.1

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
autoPROCdata reduction
autoPROCdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.59→50.79 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.25 / Stereochemistry target values: ML
Details: The last refinement steps were performed by refining with a translation libration screw (TLS) with hydrogens modelled in the riding position. Hydrogens were omitted in the final deposited model.
RfactorNum. reflection% reflection
Rfree0.1779 5813 5.01 %
Rwork0.1616 --
obs0.1624 115999 75.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.29 Å2
Refinement stepCycle: LAST / Resolution: 1.59→50.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9306 0 128 1504 10938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_angle_d1.467
X-RAY DIFFRACTIONf_dihedral_angle_d14.4133649
X-RAY DIFFRACTIONf_chiral_restr0.0961455
X-RAY DIFFRACTIONf_plane_restr0.0191683
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.610.483210.229524X-RAY DIFFRACTION0
1.61-1.630.363840.2774158X-RAY DIFFRACTION3
1.63-1.650.3366270.3033393X-RAY DIFFRACTION8
1.65-1.670.3224410.2912689X-RAY DIFFRACTION15
1.67-1.690.3571660.29781121X-RAY DIFFRACTION23
1.69-1.720.2773980.28251550X-RAY DIFFRACTION33
1.72-1.740.27181200.27492284X-RAY DIFFRACTION47
1.74-1.770.26971610.24732999X-RAY DIFFRACTION63
1.77-1.80.27261750.23643321X-RAY DIFFRACTION68
1.8-1.830.23131840.22223524X-RAY DIFFRACTION73
1.83-1.860.24761840.21363703X-RAY DIFFRACTION77
1.86-1.890.21132140.21363844X-RAY DIFFRACTION80
1.89-1.930.21872220.20374085X-RAY DIFFRACTION84
1.93-1.970.20192300.17774325X-RAY DIFFRACTION90
1.97-2.010.21092230.174702X-RAY DIFFRACTION97
2.01-2.060.20012620.17194813X-RAY DIFFRACTION100
2.06-2.110.18522640.16924792X-RAY DIFFRACTION100
2.11-2.160.15812610.15614859X-RAY DIFFRACTION100
2.16-2.230.15482540.15314849X-RAY DIFFRACTION100
2.23-2.30.15892400.14054873X-RAY DIFFRACTION100
2.3-2.380.17162550.14324838X-RAY DIFFRACTION100
2.38-2.480.15552700.15094862X-RAY DIFFRACTION100
2.48-2.590.16292380.15344869X-RAY DIFFRACTION100
2.59-2.730.17092600.15624873X-RAY DIFFRACTION100
2.73-2.90.172500.15354882X-RAY DIFFRACTION100
2.9-3.120.16852730.1544878X-RAY DIFFRACTION100
3.12-3.440.16072410.14994943X-RAY DIFFRACTION100
3.44-3.930.15192600.13284934X-RAY DIFFRACTION100
3.93-4.950.14622590.13025028X-RAY DIFFRACTION100
4.95-50.790.19452760.18095171X-RAY DIFFRACTION100

+
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