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- PDB-9g7j: Crystal structure of the tungsten-dependent aldehyde:ferredoxin o... -

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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: To Be Published
Title: Carbon monoxide-driven bioethanol production operates via 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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

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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

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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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: /

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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

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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

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