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- PDB-1n5w: Crystal Structure of the Cu,Mo-CO Dehydrogenase (CODH); Oxidized form -

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Basic information

Entry
Database: PDB / ID: 1n5w
TitleCrystal Structure of the Cu,Mo-CO Dehydrogenase (CODH); Oxidized form
Components(Carbon monoxide dehydrogenase ...) x 3
KeywordsOXIDOREDUCTASE / molybdopterin / molybdenum / MCD
Function / homology
Function and homology information


aerobic carbon monoxide dehydrogenase / carbon-monoxide oxygenase activity / anaerobic carbon-monoxide dehydrogenase activity / molybdenum ion binding / FAD binding / 2 iron, 2 sulfur cluster binding / iron ion binding / copper ion binding / metal ion binding
Similarity search - Function
Carbon-monoxide dehydrogenase, large subunit / : / : / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / [2Fe-2S]-binding domain / CO dehydrogenase flavoprotein C-terminal domain / Aldehyde Oxidoreductase; domain 4 / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain / Molybdopterin dehydrogenase, FAD-binding / CO dehydrogenase flavoprotein, C-terminal ...Carbon-monoxide dehydrogenase, large subunit / : / : / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / [2Fe-2S]-binding domain / CO dehydrogenase flavoprotein C-terminal domain / Aldehyde Oxidoreductase; domain 4 / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain / Molybdopterin dehydrogenase, FAD-binding / CO dehydrogenase flavoprotein, C-terminal / CO dehydrogenase flavoprotein, C-terminal domain superfamily / FAD binding domain in molybdopterin dehydrogenase / CO dehydrogenase flavoprotein C-terminal domain / CO dehydrogenase flavoprotein, C-terminal domain / Aldehyde oxidase/xanthine dehydrogenase / Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / [2Fe-2S]-binding / Aldehyde oxidase/xanthine dehydrogenase, first molybdopterin binding domain / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead superfamily / [2Fe-2S]-binding domain superfamily / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain superfamily / Aldehyde oxidase/xanthine dehydrogenase, second molybdopterin binding domain / [2Fe-2S] binding domain / Molybdopterin cofactor-binding domain / Molybdopterin cofactor-binding domain / Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / Aldehyde Oxidoreductase; domain 3 / FAD-binding, type PCMH, subdomain 1 / Beta-grasp domain / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / 2Fe-2S iron-sulfur cluster binding domain / Enolase-like; domain 1 / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / DNA polymerase; domain 1 / Ubiquitin-like (UB roll) / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CU(I)-S-MO(VI)(=O)OH CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / PTERIN CYTOSINE DINUCLEOTIDE / PHOSPHATE ION / Carbon monoxide dehydrogenase large chain / Carbon monoxide dehydrogenase medium chain / Carbon monoxide dehydrogenase small chain
Similarity search - Component
Biological speciesOligotropha carboxidovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsDobbek, H. / Gremer, L. / Kiefersauer, R. / Huber, R. / Meyer, O.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Catalysis at a dinuclear [CuSMo(=O)OH] cluster in a CO dehydrogenase resolved at 1.1-A resolution
Authors: Dobbek, H. / Gremer, L. / Kiefersauer, R. / Huber, R. / Meyer, O.
History
DepositionNov 7, 2002Deposition site: RCSB / Processing site: PDBJ
SupersessionDec 23, 2002ID: 1QJ2
Revision 1.0Dec 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbon monoxide dehydrogenase small chain
B: Carbon monoxide dehydrogenase large chain
C: Carbon monoxide dehydrogenase medium chain
D: Carbon monoxide dehydrogenase small chain
E: Carbon monoxide dehydrogenase large chain
F: Carbon monoxide dehydrogenase medium chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)278,08117
Polymers273,8696
Non-polymers4,21111
Water44,6592479
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27060 Å2
ΔGint-217 kcal/mol
Surface area79030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.295, 132.088, 159.825
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Carbon monoxide dehydrogenase ... , 3 types, 6 molecules ADBECF

#1: Protein Carbon monoxide dehydrogenase small chain / CO dehydrogenase subunit S


Mass: 17810.428 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oligotropha carboxidovorans (bacteria) / Strain: OM5
References: UniProt: P19921, carbon-monoxide dehydrogenase (acceptor)
#2: Protein Carbon monoxide dehydrogenase large chain / CO dehydrogenase subunit L


Mass: 88847.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oligotropha carboxidovorans (bacteria) / Strain: OM5
References: UniProt: P19919, carbon-monoxide dehydrogenase (acceptor)
#3: Protein Carbon monoxide dehydrogenase medium chain / CO dehydrogenase subunit M


Mass: 30276.939 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oligotropha carboxidovorans (bacteria) / Strain: OM5
References: UniProt: P19920, carbon-monoxide dehydrogenase (acceptor)

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Non-polymers , 6 types, 2490 molecules

#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#6: Chemical ChemComp-CUM / CU(I)-S-MO(VI)(=O)OH CLUSTER


Mass: 224.558 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CuHMoO2S
#7: Chemical ChemComp-MCN / PTERIN CYTOSINE DINUCLEOTIDE


Mass: 696.501 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H22N8O13P2S2
#8: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2479 / 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: 2.3 Å3/Da / Density % sol: 46.47 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: sodium, potassium phospate, HEPES, MPD, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Crystal grow
*PLUS
Method: vapor diffusion
Details: Dobbek, H., (1999) Proc.Natl.Acad.Sci.USA, 96, 8884.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.8 M11KH2PO4
20.8 M11NaH2PO4
32 %MPD11
4100 mMHEPES11pH7.3

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 14, 1999
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.49→20 Å / Num. all: 387014 / Num. obs: 387014 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.49→1.52 Å / % possible all: 65.6
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 941420 / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
Mean I/σ(I) obs: 3.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
REFMACrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→18 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.171 19010 RANDOM
Rwork0.135 --
all0.135 358402 -
obs0.135 358402 -
Refinement stepCycle: LAST / Resolution: 1.5→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18918 0 155 2479 21552
Refinement
*PLUS
Lowest resolution: 18 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.946
LS refinement shell
*PLUS
Rfactor Rfree: 0.2 / Rfactor Rwork: 0.13

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