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- PDB-4udx: CO2 bound to cluster C of Ni,Fe-CO dehydrogenase at true-atomic r... -

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Basic information

Entry
Database: PDB / ID: 4udx
TitleCO2 bound to cluster C of Ni,Fe-CO dehydrogenase at true-atomic resolution
ComponentsCARBON MONOXIDE DEHYDROGENASE 2
KeywordsOXIDOREDUCTASE
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
CARBON DIOXIDE / : / 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 / MOLECULAR REPLACEMENT / Resolution: 1.03 Å
AuthorsFesseler, J. / Jeoung, J.-H. / Dobbek, H.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2015
Title: How the [NiFe4S4] Cluster of CO Dehydrogenase Activates CO2 and NCO(-).
Authors: Fesseler, J. / Jeoung, J.H. / Dobbek, H.
History
DepositionDec 12, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Jul 5, 2017Group: Refinement description / Category: software
Revision 2.0Jan 23, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / pdbx_struct_conn_angle
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] / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _pdbx_struct_conn_angle.value
Revision 2.1May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 2.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_label_atom_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)67,9746
Polymers66,9921
Non-polymers9825
Water14,034779
1
X: CARBON MONOXIDE DEHYDROGENASE 2
hetero molecules

X: CARBON MONOXIDE DEHYDROGENASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,94912
Polymers133,9852
Non-polymers1,96410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area9780 Å2
ΔGint-202.9 kcal/mol
Surface area38060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.516, 74.870, 71.075
Angle α, β, γ (deg.)90.00, 111.26, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11X-2091-

HOH

21X-2339-

HOH

31X-2396-

HOH

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Components

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Protein , 1 types, 1 molecules X

#1: Protein CARBON MONOXIDE DEHYDROGENASE 2 / / CODH 2 / NI / FE-CO DEHYDROGENASE


Mass: 66992.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CARBOXYDOTHERMUS HYDROGENOFORMANS (bacteria)
Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q9F8A8, carbon-monoxide dehydrogenase (acceptor)

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Non-polymers , 6 types, 784 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.: 1 / Source method: obtained synthetically / Formula: Fe
#6: Chemical ChemComp-CO2 / CARBON DIOXIDE / Carbon dioxide


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 779 / 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: 2.08 Å3/Da / Density % sol: 40.93 % / Description: NONE
Crystal growpH: 8 / Details: PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841
DetectorType: RAYONICS / Detector: CCD / Date: Jun 12, 2013 / Details: MIRRORS
RadiationMonochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.03→28.11 Å / Num. obs: 264706 / % possible obs: 98 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.39
Reflection shellResolution: 1.03→1.07 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 1.71 / % possible all: 82.2

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Processing

Software
NameVersionClassification
SHELXL14refinement
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.03→50 Å / Num. parameters: 50029 / Num. restraintsaints: 56542 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 4
RfactorNum. reflection% reflectionSelection details
Rfree0.1565 13236 5 %RANDOM
all0.132 251470 --
obs0.132 -93.1 %-
Refine analyzeNum. disordered residues: 23 / Occupancy sum hydrogen: 4625 / Occupancy sum non hydrogen: 5397.05
Refinement stepCycle: LAST / Resolution: 1.03→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4653 0 24 779 5456
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.0462
X-RAY DIFFRACTIONs_angle_d0.0425
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.006
X-RAY DIFFRACTIONs_zero_chiral_vol0.0867
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.0925
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.2335
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.0482
X-RAY DIFFRACTIONs_approx_iso_adps0.1837

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