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- PDB-3i39: NI,FE-CODH-320 MV+CN state -

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Basic information

Entry
Database: PDB / ID: 3i39
TitleNI,FE-CODH-320 MV+CN state
ComponentsCarbon monoxide dehydrogenase 2
KeywordsOXIDOREDUCTASE / CYANIDE / CLUSTER C / IRON / IRON-SULFUR / MEMBRANE / METAL-BINDING / NICKEL / Cell inner membrane / Cell membrane
Function / homology
Function and homology information


anaerobic carbon monoxide dehydrogenase / carbon-monoxide dehydrogenase (ferredoxin) activity / carbon-monoxide dehydrogenase (acceptor) activity / nickel cation binding / generation of precursor metabolites and energy / 4 iron, 4 sulfur cluster binding / plasma membrane / cytoplasm
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #30 / Rossmann fold - #2030 / 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 / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #30 / Rossmann fold - #2030 / 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 / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CYANIDE ION / : / FE2/S2 (INORGANIC) CLUSTER / IRON/SULFUR CLUSTER / FE(3)-NI(1)-S(4) CLUSTER / Carbon monoxide dehydrogenase 2
Similarity search - Component
Biological speciesCarboxydothermus hydrogenoformans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.36 Å
AuthorsJeoung, J.-H. / Dobbek, H.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: Structural basis of cyanide inhibition of Ni, Fe-containing carbon monoxide dehydrogenase
Authors: Jeoung, J.H. / Dobbek, H.
History
DepositionJun 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Carbon monoxide dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2127
Polymers69,1921
Non-polymers1,0206
Water16,033890
1
X: Carbon monoxide dehydrogenase 2
hetero molecules

X: Carbon monoxide dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,42314
Polymers138,3842
Non-polymers2,03912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area6950 Å2
ΔGint-39 kcal/mol
Surface area38640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.279, 75.834, 71.099
Angle α, β, γ (deg.)90.00, 111.33, 90.00
Int Tables number5
Space group name H-MC121
Details-X,Y,-Z

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Components

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Protein , 1 types, 1 molecules X

#1: Protein Carbon monoxide dehydrogenase 2 / / CODH 2


Mass: 69191.891 Da / Num. of mol.: 1 / Mutation: K3R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans (bacteria)
Strain: Z-2901 / Gene: CHY_0085, cooS2, cooSII / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): ROSSETTA DE3
References: UniProt: Q9F8A8, carbon-monoxide dehydrogenase (acceptor)

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Non-polymers , 6 types, 896 molecules

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


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#4: Chemical ChemComp-WCC / FE(3)-NI(1)-S(4) CLUSTER / C CLUSTER CUBANE


Mass: 354.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3NiS4
#5: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#6: Chemical ChemComp-CYN / CYANIDE ION / Cyanide


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 890 / Source method: isolated from a natural source / Formula: H2O

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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: 2.02 Å3/Da / Density % sol: 39.09 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% PEG 3350, 0.2 M Ammonium sulfate, 0.1 M Bis-Tris pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: MX-225 / Detector: CCD / Date: Feb 16, 2009
RadiationMonochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.36→35 Å / Num. all: 119149 / Num. obs: 116242 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Net I/σ(I): 14.12
Reflection shellResolution: 1.36→1.4 Å / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CNSrefinement
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.36→30.6 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.063 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19019 5757 5 %RANDOM
Rwork0.15375 ---
obs0.15557 109407 97.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.413 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å2-0 Å2-0.68 Å2
2--0.36 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.36→30.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4670 0 24 890 5584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0225218
X-RAY DIFFRACTIONr_bond_other_d00.023443
X-RAY DIFFRACTIONr_angle_refined_deg1.9861.9927262
X-RAY DIFFRACTIONr_angle_other_deg1.4938597
X-RAY DIFFRACTIONr_dihedral_angle_1_deg75758
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.69325.174201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04415915
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9591528
X-RAY DIFFRACTIONr_chiral_restr0.1710.2868
X-RAY DIFFRACTIONr_gen_planes_refined0.0250.0215957
X-RAY DIFFRACTIONr_gen_planes_other0.0320.02934
X-RAY DIFFRACTIONr_mcbond_it2.8441.53386
X-RAY DIFFRACTIONr_mcbond_other1.1521.51377
X-RAY DIFFRACTIONr_mcangle_it3.95425530
X-RAY DIFFRACTIONr_scbond_it6.49931797
X-RAY DIFFRACTIONr_scangle_it8.6234.51557
X-RAY DIFFRACTIONr_rigid_bond_restr1.233310
X-RAY DIFFRACTIONr_sphericity_free36.6132
X-RAY DIFFRACTIONr_sphericity_bonded5.684310
LS refinement shellResolution: 1.36→1.395 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 417 -
Rwork0.265 7948 -
obs--96.04 %

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