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- PDB-3b51: Ni,Fe-CODH-600 mV state -

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Basic information

Entry
Database: PDB / ID: 3b51
TitleNi,Fe-CODH-600 mV state
ComponentsCarbon monoxide dehydrogenase 2
KeywordsOXIDOREDUCTASE / cluster C / 4Fe-4S / Cytoplasm / Iron / Iron-sulfur / Membrane / Metal-binding / Nickel
Function / homology
Function and homology information


anaerobic carbon monoxide dehydrogenase / hydroxylamine reductase activity / anaerobic carbon-monoxide dehydrogenase activity / nickel cation binding / response to hydrogen peroxide / peroxidase activity / 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
FE2/S2 (INORGANIC) CLUSTER / IRON/SULFUR CLUSTER / FE(4)-NI(1)-S(4) CLUSTER / Carbon monoxide dehydrogenase 2
Similarity search - Component
Biological speciesCarboxydothermus hydrogenoformans Z-2901 (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.4 Å
AuthorsJeoung, J.H. / Dobbek, H.
CitationJournal: Science / Year: 2007
Title: Carbon dioxide activation at the Ni,Fe-cluster of anaerobic carbon monoxide dehydrogenase.
Authors: Jeoung, J.H. / Dobbek, H.
History
DepositionOct 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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 2.0Aug 12, 2026Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _chem_comp_atom.atom_id / _chem_comp_atom.comp_id / _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_atom.pdbx_stereo_config / _chem_comp_atom.type_symbol / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.comp_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id
Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Carbon monoxide dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1304
Polymers69,1921
Non-polymers9383
Water15,925884
1
X: Carbon monoxide dehydrogenase 2
hetero molecules

X: Carbon monoxide dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,2598
Polymers138,3842
Non-polymers1,8766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area8380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.750, 74.660, 70.650
Angle α, β, γ (deg.)90.00, 111.28, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11X-1067-

HOH

21X-1755-

HOH

31X-1769-

HOH

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Components

#1: Protein Carbon monoxide dehydrogenase 2 / CODH 2


Mass: 69191.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans Z-2901 (bacteria)
Species: Carboxydothermus hydrogenoformans / Strain: Z-2901 / DSM 6008 / Gene: cooS2, cooSII / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta DE3
References: UniProt: Q9F8A8, carbon-monoxide dehydrogenase (acceptor)
#2: Chemical ChemComp-SF4 / 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


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


Mass: 410.333 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4NiS4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 884 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.98 Å3/Da / Density % sol: 38.02 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG3350, (NH4)2SO4, Bis-Tris, sodium dithionite, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 2007 / Details: Osmic mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.4→27.9 Å / Num. obs: 104078 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 14.233 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 15.72
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 0.188 / Mean I/σ(I) obs: 3.5 / Num. measured obs: 4114 / Num. unique obs: 9062 / % possible all: 85.8

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
MAR345dtbdata collection
CNSphasing
RefinementResolution: 1.4→27.9 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.159 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.183 5229 5 %RANDOM
Rwork0.157 ---
obs0.158 104078 97.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.523 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å2-0.27 Å2
2--0.08 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.4→27.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4750 0 22 884 5656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0434881
X-RAY DIFFRACTIONr_bond_other_d0.0180.0283186
X-RAY DIFFRACTIONr_angle_refined_deg1.916.7276706
X-RAY DIFFRACTIONr_angle_other_deg1.7413.9437903
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.755671
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.54525.028181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.02915833
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6611525
X-RAY DIFFRACTIONr_chiral_restr0.0960.2807
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025464
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02857
X-RAY DIFFRACTIONr_nbd_refined0.2110.21183
X-RAY DIFFRACTIONr_nbd_other0.1930.23666
X-RAY DIFFRACTIONr_nbtor_refined0.1690.22477
X-RAY DIFFRACTIONr_nbtor_other0.0870.22479
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2782
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0070.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1490.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.235
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2530.299
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.2105
X-RAY DIFFRACTIONr_mcbond_it0.6861.54163
X-RAY DIFFRACTIONr_mcbond_other0.1261.51314
X-RAY DIFFRACTIONr_mcangle_it0.78125164
X-RAY DIFFRACTIONr_scbond_it1.64531850
X-RAY DIFFRACTIONr_scangle_it2.2694.51456
X-RAY DIFFRACTIONr_rigid_bond_restr1.855310
X-RAY DIFFRACTIONr_sphericity_bonded2.765312
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 355 -
Rwork0.326 6290 -
all-6645 -
obs--84.8 %

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