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- PDB-3b53: Ni,Fe-CODH-320 mV state -

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Basic information

Entry
Database: PDB / ID: 3b53
TitleNi,Fe-CODH-320 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 / 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
: / FE2/S2 (INORGANIC) CLUSTER / IRON/SULFUR CLUSTER / FE(3)-NI(1)-S(4) CLUSTER / Carbon monoxide dehydrogenase 2
Similarity search - Component
Biological speciesCarboxydothermus hydrogenoformans Z-2901 (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.5 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 2.0Apr 22, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_distant_solvent_atoms / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
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_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] / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details
Revision 2.1Feb 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 / struct_conn / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)70,1305
Polymers69,1921
Non-polymers9384
Water15,925884
1
X: Carbon monoxide dehydrogenase 2
hetero molecules

X: Carbon monoxide dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,25910
Polymers138,3842
Non-polymers1,8768
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area8340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.830, 74.520, 70.740
Angle α, β, γ (deg.)90.000, 111.400, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11X-1756-

HOH

21X-1770-

HOH

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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
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)

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Non-polymers , 5 types, 888 molecules

#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


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


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 884 / 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: 1.98 Å3/Da / Density % sol: 37.98 %
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 18, 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
ReflectionHighest resolution: 1.48 Å / Num. obs: 81496 / % possible obs: 90.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.262 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 13.76
Reflection shellResolution: 1.48→1.5 Å / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 5.3 / Num. measured obs: 11557 / Num. unique obs: 2994 / % possible all: 85.1

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
MAR345dtbdata collection
RefinementResolution: 1.5→26.66 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.753 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.178 2360 3 %RANDOM
Rwork0.145 ---
obs0.146 78501 90.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.261 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å2-1.34 Å2
2---0.96 Å20 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 1.5→26.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4748 0 22 884 5654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0434879
X-RAY DIFFRACTIONr_bond_other_d0.0020.023181
X-RAY DIFFRACTIONr_angle_refined_deg1.9516.736703
X-RAY DIFFRACTIONr_angle_other_deg0.92537888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8265671
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.04225180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.10315833
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9691525
X-RAY DIFFRACTIONr_chiral_restr0.0980.2807
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025460
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02857
X-RAY DIFFRACTIONr_nbd_refined0.2110.21242
X-RAY DIFFRACTIONr_nbd_other0.1960.23786
X-RAY DIFFRACTIONr_nbtor_refined0.1710.22473
X-RAY DIFFRACTIONr_nbtor_other0.0880.22494
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2769
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0270.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1760.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.235
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2520.2103
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.296
X-RAY DIFFRACTIONr_mcbond_it0.7061.54147
X-RAY DIFFRACTIONr_mcbond_other0.1431.51314
X-RAY DIFFRACTIONr_mcangle_it0.81325164
X-RAY DIFFRACTIONr_scbond_it1.73731848
X-RAY DIFFRACTIONr_scangle_it2.3634.51453
X-RAY DIFFRACTIONr_rigid_bond_restr2.241310
X-RAY DIFFRACTIONr_sphericity_bonded5.342312
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 168 -
Rwork0.249 5312 -
all-5480 -
obs--85.67 %

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