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- PDB-6yu9: CO-dehydrogenase homodimer from Clostridium autoethanogenum at 1.... -

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Basic information

Entry
Database: PDB / ID: 6yu9
TitleCO-dehydrogenase homodimer from Clostridium autoethanogenum at 1.90-A resolution
ComponentsCarbon-monoxide dehydrogenase (Acceptor),Carbon-monoxide dehydrogenase (Acceptor)
KeywordsOXIDOREDUCTASE / C1-Metabolism / Carbon monoxide / metallo-containing protein / Acetogenic bacteria / Acetogenesis / CO-dehydrogenase/Acetyl-CoA synthase / X-ray crystal structure / Gas channeling / Waste-gas conversion
Function / homology
Function and homology information


carbon-monoxide dehydrogenase (acceptor) / : / nickel cation binding / generation of precursor metabolites and energy / 4 iron, 4 sulfur cluster binding
Similarity search - Function
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 / IRON/SULFUR CLUSTER / FE(4)-NI(1)-S(4) CLUSTER / Carbon-monoxide dehydrogenase (Acceptor)
Similarity search - Component
Biological speciesClostridium autoethanogenum DSM 10061 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.904 Å
AuthorsWagner, T. / Lemaire, O.N.
Funding support Germany, 2items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)DFG-SPP 1927 WA 4053/1-1 Germany
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2020
Title: Gas channel rerouting in a primordial enzyme: Structural insights of the carbon-monoxide dehydrogenase/acetyl-CoA synthase complex from the acetogen Clostridium autoethanogenum.
Authors: Lemaire, O.N. / Wagner, T.
History
DepositionApr 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jan 24, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbon-monoxide dehydrogenase (Acceptor),Carbon-monoxide dehydrogenase (Acceptor)
B: Carbon-monoxide dehydrogenase (Acceptor),Carbon-monoxide dehydrogenase (Acceptor)
C: Carbon-monoxide dehydrogenase (Acceptor),Carbon-monoxide dehydrogenase (Acceptor)
D: Carbon-monoxide dehydrogenase (Acceptor),Carbon-monoxide dehydrogenase (Acceptor)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)276,11622
Polymers271,9104
Non-polymers4,20618
Water19,9431107
1
A: Carbon-monoxide dehydrogenase (Acceptor),Carbon-monoxide dehydrogenase (Acceptor)
B: Carbon-monoxide dehydrogenase (Acceptor),Carbon-monoxide dehydrogenase (Acceptor)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,12912
Polymers135,9552
Non-polymers2,17410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10210 Å2
ΔGint-149 kcal/mol
Surface area39800 Å2
MethodPISA
2
C: Carbon-monoxide dehydrogenase (Acceptor),Carbon-monoxide dehydrogenase (Acceptor)
D: Carbon-monoxide dehydrogenase (Acceptor),Carbon-monoxide dehydrogenase (Acceptor)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,98710
Polymers135,9552
Non-polymers2,0328
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9720 Å2
ΔGint-164 kcal/mol
Surface area39480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.531, 109.446, 129.280
Angle α, β, γ (deg.)90.000, 112.550, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Carbon-monoxide dehydrogenase (Acceptor),Carbon-monoxide dehydrogenase (Acceptor)


Mass: 67977.531 Da / Num. of mol.: 4 / Mutation: Wild-type / Source method: isolated from a natural source
Details: A stop codon is present in the gene and the CODH seems to be split in two peptides. However, experimental evidence proved that a stop codon read-through occurs leading to a cysteine (C401). ...Details: A stop codon is present in the gene and the CODH seems to be split in two peptides. However, experimental evidence proved that a stop codon read-through occurs leading to a cysteine (C401).,A stop codon is present in the gene and the CODH seems to be split in two peptides. However, experimental evidence proved that a stop codon read-through occurs leading to a cysteine (C401).
Source: (natural) Clostridium autoethanogenum DSM 10061 (bacteria)
Cell line: / / Organ: / / Plasmid details: / / Variant: / / Tissue: /
References: UniProt: U5RTE2, carbon-monoxide dehydrogenase (acceptor)

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Non-polymers , 6 types, 1125 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 6 / 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 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1107 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.56 Å3/Da / Density % sol: 52.05 % / Description: Brownish thick quadratic plates
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: Crystallization was performed in an anoxic chamber (N2/H2, 95:5 %) with anaerobic solutions. Crystals were obtained by initial screening at 291.15 K using the sitting drop method on a 96- ...Details: Crystallization was performed in an anoxic chamber (N2/H2, 95:5 %) with anaerobic solutions. Crystals were obtained by initial screening at 291.15 K using the sitting drop method on a 96-well MRC 2 Crystallization Plates in polystyrene (SWISSCI). The crystallization reservoir contained 90 uL of mother liquor, crystallization drop contained a mixture of 0.6 uL protein and 0.6 uL precipitant. The protein concentration was 16.9 mg/mL in 25 mM Tris/HCl pH7.6, 10% glycerol (v/v) and 2 mM dithiothreitol. The best diffracting crystal of CODH was obtained by initial screening using the Shotgun (SG1) screen from Molecular dimensions. The crystallization reservoir contained 200 mM Magnesium acetate tetrahydrate; 20% (w/v) polyethylene glycol 3350. Crystals were cryo protected in the same solution supplemented with 25% glycerol (v/v).
Temp details: Fluctuation of 1 K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.9→119.4 Å / Num. obs: 102786 / % possible obs: 93.3 % / Redundancy: 6.2 % / CC1/2: 0.993 / Rmerge(I) obs: 0.205 / Rpim(I) all: 0.088 / Rrim(I) all: 0.223 / Net I/σ(I): 7.7
Reflection shellResolution: 1.9→2.179 Å / Redundancy: 4 % / Rmerge(I) obs: 0.804 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 5140 / CC1/2: 0.611 / Rpim(I) all: 0.45 / Rrim(I) all: 0.928 / % possible all: 63.9

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (19-MAR-2020)refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YTT

6ytt


Resolution: 1.904→49.75 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.911 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.372 / SU Rfree Blow DPI: 0.216
RfactorNum. reflection% reflectionSelection details
Rfree0.2026 5293 5.15 %RANDOM
Rwork0.1575 ---
obs0.1598 102786 48 %-
Displacement parametersBiso max: 136.93 Å2 / Biso mean: 33.12 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-1.5935 Å20 Å22.0385 Å2
2--2.2535 Å20 Å2
3----3.847 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: final / Resolution: 1.904→49.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18851 0 113 1107 20071
Biso mean--32.34 31.26 -
Num. residues----2512
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d11753SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes6081HARMONIC10
X-RAY DIFFRACTIONt_it19329HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2592SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact31692SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d38551HARMONIC50.011
X-RAY DIFFRACTIONt_angle_deg70222HARMONIC51.12
X-RAY DIFFRACTIONt_omega_torsion3.58
X-RAY DIFFRACTIONt_other_torsion16.32
LS refinement shellResolution: 1.904→2.07 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2411 92 4.47 %
Rwork0.2028 1964 -
obs--4.37 %
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)
10.46980.0226-0.11340-0.00340.4159-0.0240.0522-0.01370.0505-0.01870.00550.0213-0.04510.04270.0122-0.00810.0281-0.0561-0.0248-0.07581.1318-2.906720.4997
20.47380.0357-0.27160.00150.03590.4588-0.02440.1023-0.01650.0346-0.01510.01680.01450.11830.0395-0.04780.0187-0.00080.03010.0359-0.110639.27433.63437.4694
30.9175-0.0693-0.221100.20050.3389-0.0137-0.03680.148-0.05970.05930.11490.12120.2302-0.0456-0.05910.07660.05130.07380.0054-0.142828.1962-54.643540.4066
40.6414-0.2818-0.38760-0.07220.6157-0.0138-0.12230.0433-0.05470.01980.02490.04970.0335-0.0060.0038-0.00130.0107-0.05990.006-0.1017-10.7506-51.424351.9846
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 631
2X-RAY DIFFRACTION2{ B|* }B4 - 631
3X-RAY DIFFRACTION3{ C|* }C4 - 631
4X-RAY DIFFRACTION4{ D|* }D4 - 631

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