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- PDB-1suf: Carbon Monoxide Dehydrogenase from Carboxydothermus hydrogenoform... -

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Basic information

Entry
Database: PDB / ID: 1suf
TitleCarbon Monoxide Dehydrogenase from Carboxydothermus hydrogenoformans-Inactive state
ComponentsCarbon Monoxide Dehydrogenase 2
KeywordsOXIDOREDUCTASE / CODH / carbon monoxide dehydrogenase / nickel / cluster C
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 / FE(4)-NI(1)-S(5) CLUSTER / IRON/SULFUR CLUSTER / Carbon monoxide dehydrogenase 2
Similarity search - Component
Biological speciesCarboxydothermus hydrogenoformans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsDobbek, H. / Svetlitchnyi, V. / Liss, J. / Meyer, O.
CitationJournal: J.Am.Chem.Soc. / Year: 2004
Title: Carbon Monoxide Induced Decomposition of the Active Site [Ni-4Fe-5S] Cluster of CO Dehydrogenase
Authors: Dobbek, H. / Svetlitchnyi, V. / Liss, J. / Meyer, O.
History
DepositionMar 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / 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.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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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
Remark 999SEQUENCE AUTHORS INFORMED THAT THE COMPLETE SEQUENCE OF CARBOXYDOTHERMUS HYDROGENOFORMANS HAS BEEN ...SEQUENCE AUTHORS INFORMED THAT THE COMPLETE SEQUENCE OF CARBOXYDOTHERMUS HYDROGENOFORMANS HAS BEEN DETERMINED AND THAT THE PRELIMINARY RESULTS ARE AVAILABLE THROUGH THE TIGR HOME PAGE (WWW.TIGR.ORG).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbon Monoxide Dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9624
Polymers66,9921
Non-polymers9703
Water19,1501063
1
A: Carbon Monoxide Dehydrogenase 2
hetero molecules

A: Carbon Monoxide Dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,9258
Polymers133,9852
Non-polymers1,9406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area9360 Å2
ΔGint-179 kcal/mol
Surface area38250 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)112.614, 75.004, 71.374
Angle α, β, γ (deg.)90.00, 110.97, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1419-

HOH

21A-1424-

HOH

31A-1600-

HOH

DetailsThe second part of the biological assembly is generated by the two fold axis: -x, y, -z.

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Components

#1: Protein Carbon Monoxide Dehydrogenase 2 / / CODH 2


Mass: 66992.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Carboxydothermus hydrogenoformans (bacteria)
References: UniProt: Q9F8A8, carbon-monoxide dehydrogenase (acceptor)
#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-NFS / FE(4)-NI(1)-S(5) CLUSTER


Mass: 442.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4NiS5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1063 / 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: 2.1 Å3/Da / Density % sol: 41.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3000, 2-Propanol, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 2003
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.15→20 Å / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameClassification
MAR345data collection
XDSdata reduction
CNSrefinement
SHELXL-97refinement
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.15→8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.1902 9071 RANDOM
Rwork0.1519 --
all0.1521 181214 -
obs0.1521 181214 -
Refinement stepCycle: LAST / Resolution: 1.15→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4653 0 21 1063 5737

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