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- PDB-1jqk: Crystal structure of carbon monoxide dehydrogenase from Rhodospir... -

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Basic information

Entry
Database: PDB / ID: 1jqk
TitleCrystal structure of carbon monoxide dehydrogenase from Rhodospirillum rubrum
Componentscarbon monoxide dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann fold
Function / homology
Function and homology information


anaerobic carbon monoxide dehydrogenase / hydroxylamine reductase activity / anaerobic carbon-monoxide dehydrogenase activity / 3 iron, 4 sulfur cluster binding / nickel cation binding / generation of precursor metabolites and energy / peroxidase activity / response to hydrogen peroxide / ferrous iron binding / 4 iron, 4 sulfur cluster binding ...anaerobic carbon monoxide dehydrogenase / hydroxylamine reductase activity / anaerobic carbon-monoxide dehydrogenase activity / 3 iron, 4 sulfur cluster binding / nickel cation binding / generation of precursor metabolites and energy / peroxidase activity / response to hydrogen peroxide / ferrous iron binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / protein homodimerization activity / protein-containing complex / 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
: / IRON/SULFUR CLUSTER / FE(3)-NI(1)-S(4) CLUSTER / Carbon monoxide dehydrogenase
Similarity search - Component
Biological speciesRhodospirillum rubrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsDrennan, C.L. / Heo, J. / Sintchak, M.D. / Schreiter, E. / Ludden, P.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Life on carbon monoxide: X-ray structure of Rhodospirillum rubrum Ni-Fe-S carbon monoxide dehydrogenase.
Authors: Drennan, C.L. / Heo, J. / Sintchak, M.D. / Schreiter, E. / Ludden, P.W.
History
DepositionAug 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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_database_remark / 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_database_remark.text / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_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_asym_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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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_asym_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN The ligand WCC is a Ni-Fe-S cubane. There is an unidentified ligand, UNX, bound to the Ni ...HETEROGEN The ligand WCC is a Ni-Fe-S cubane. There is an unidentified ligand, UNX, bound to the Ni of the WCC. There is also a FE2 bound to the cubane. The C-cluster, as it is called, has a single iron site (FE2) and a four-metal cubane (Ni-Fe-S).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: carbon monoxide dehydrogenase
B: carbon monoxide dehydrogenase
C: carbon monoxide dehydrogenase
D: carbon monoxide dehydrogenase
E: carbon monoxide dehydrogenase
F: carbon monoxide dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)407,19533
Polymers401,5686
Non-polymers5,62727
Water00
1
A: carbon monoxide dehydrogenase
B: carbon monoxide dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,73211
Polymers133,8562
Non-polymers1,8769
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10000 Å2
ΔGint-163 kcal/mol
Surface area36070 Å2
MethodPISA
2
C: carbon monoxide dehydrogenase
D: carbon monoxide dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,73211
Polymers133,8562
Non-polymers1,8769
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9920 Å2
ΔGint-161 kcal/mol
Surface area35960 Å2
MethodPISA
3
E: carbon monoxide dehydrogenase
F: carbon monoxide dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,73211
Polymers133,8562
Non-polymers1,8769
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9910 Å2
ΔGint-160 kcal/mol
Surface area36150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.6, 200.1, 116.8
Angle α, β, γ (deg.)90.0, 111.5, 90.0
Int Tables number4
Space group name H-MP1211
DetailsThe homodimer is the biological unit.

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Components

#1: Protein
carbon monoxide dehydrogenase / CODH


Mass: 66927.969 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: COOS gene / Source: (natural) Rhodospirillum rubrum (bacteria)
References: UniProt: P31896, carbon-monoxide dehydrogenase (acceptor)
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical
ChemComp-WCC / FE(3)-NI(1)-S(4) CLUSTER / C CLUSTER CUBANE


Mass: 354.488 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe3NiS4
#5: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 6 / Source method: obtained synthetically

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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: 2.51 Å3/Da / Density % sol: 50.92 %
Crystal growTemperature: 298 K / Method: capillary crystallization / pH: 7.5
Details: 10% PEG 8000, 0.1 M Tris buffer, 0.4 M calcium chloride, 5% 2-methyl-2,4-pentanediol, pH 7.5, capillary crystallization, temperature 298.0K
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 %PEG800011
20.05 MTris11
30.2 M11CaCl2
42.5 %MPD11
510 mg/mlprotein11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.3 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Jul 30, 2000 / Details: condensing mirror
RadiationMonochromator: two crystal non-dispersive monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. obs: 90759 / % possible obs: 94 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 2.5 % / Biso Wilson estimate: 63.5 Å2 / Rsym value: 0.086 / Net I/σ(I): 8.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 7792 / Rsym value: 0.356 / % possible all: 80.8
Reflection
*PLUS
Num. measured all: 223988 / Rmerge(I) obs: 0.086
Reflection shell
*PLUS
% possible obs: 80.1 % / Rmerge(I) obs: 0.35

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Processing

Software
NameVersionClassification
SOLVEphasing
SHARPphasing
DMmodel building
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→100 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: bulk solvent correction, NCS restraints, maximum likelihood target, cartesian molecular dynamics. There are 3 homodimers in the asymmetric unit: chains A&B, C&D, and E&F. Molecules C&D, E&F ...Details: bulk solvent correction, NCS restraints, maximum likelihood target, cartesian molecular dynamics. There are 3 homodimers in the asymmetric unit: chains A&B, C&D, and E&F. Molecules C&D, E&F have lower B-factors than A&B, and are the molecules that should be considered in structural analyses. No side chain density was seen for residue 348.
RfactorNum. reflection% reflectionSelection details
Rfree0.287 3716 5 %Random
Rwork0.257 ---
all0.276 90727 --
obs0.259 74708 76.9 %-
Displacement parametersBiso mean: 47.6 Å2
Refinement stepCycle: LAST / Resolution: 2.8→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26766 0 132 0 26898
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.33
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 100 Å / σ(F): 2 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 47.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1

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