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- PDB-1ffu: CARBON MONOXIDE DEHYDROGENASE FROM HYDROGENOPHAGA PSEUDOFLAVA WHI... -

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Basic information

Entry
Database: PDB / ID: 1ffu
TitleCARBON MONOXIDE DEHYDROGENASE FROM HYDROGENOPHAGA PSEUDOFLAVA WHICH LACKS THE MO-PYRANOPTERIN MOIETY OF THE MOLYBDENUM COFACTOR
Components
  • CUTL, MOLYBDOPROTEIN OF CARBON MONOXIDE DEHYDROGENASE
  • CUTM, FLAVOPROTEIN OF CARBON MONOXIDE DEHYDROGENASE
  • CUTS, IRON-SULFUR PROTEIN OF CARBON MONOXIDE DEHYDROGENASE
KeywordsHYDROLASE / DEHYDROGENASE
Function / homology
Function and homology information


aerobic carbon monoxide dehydrogenase / carbon-monoxide oxygenase activity / carbon-monoxide dehydrogenase (acceptor) 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 / CO dehydrogenase flavoprotein, C-terminal domain / CO dehydrogenase flavoprotein C-terminal domain / Aldehyde Oxidoreductase; domain 4 / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain / [2Fe-2S]-binding domain / Molybdopterin dehydrogenase, FAD-binding / CO dehydrogenase flavoprotein, C-terminal / CO dehydrogenase flavoprotein, C-terminal domain superfamily ...Carbon-monoxide dehydrogenase, large subunit / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / CO dehydrogenase flavoprotein, C-terminal domain / CO dehydrogenase flavoprotein C-terminal domain / Aldehyde Oxidoreductase; domain 4 / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain / [2Fe-2S]-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 / Aldehyde oxidase/xanthine dehydrogenase / Aldehyde oxidase/xanthine dehydrogenase, second molybdopterin binding domain / Molybdopterin cofactor-binding domain / 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 / [2Fe-2S] 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 / FAD-binding, type PCMH, subdomain 1 / Aldehyde Oxidoreductase; domain 3 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / Beta-grasp domain superfamily / Enolase-like; domain 1 / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Ubiquitin-like (UB roll) / DNA polymerase; domain 1 / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CYTIDINE-5'-DIPHOSPHATE / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / : / Carbon monoxide dehydrogenase large chain / Carbon monoxide dehydrogenase medium chain / Carbon monoxide dehydrogenase small chain
Similarity search - Component
Biological speciesHydrogenophaga pseudoflava (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.35 Å
AuthorsHaenzelmann, P. / Dobbek, H. / Gremer, L. / Huber, R. / Meyer, O.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: The effect of intracellular molybdenum in Hydrogenophaga pseudoflava on the crystallographic structure of the seleno-molybdo-iron-sulfur flavoenzyme carbon monoxide dehydrogenase.
Authors: Hanzelmann, P. / Dobbek, H. / Gremer, L. / Huber, R. / Meyer, O.
History
DepositionJul 26, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: CUTS, IRON-SULFUR PROTEIN OF CARBON MONOXIDE DEHYDROGENASE
B: CUTL, MOLYBDOPROTEIN OF CARBON MONOXIDE DEHYDROGENASE
C: CUTM, FLAVOPROTEIN OF CARBON MONOXIDE DEHYDROGENASE
D: CUTS, IRON-SULFUR PROTEIN OF CARBON MONOXIDE DEHYDROGENASE
E: CUTL, MOLYBDOPROTEIN OF CARBON MONOXIDE DEHYDROGENASE
F: CUTM, FLAVOPROTEIN OF CARBON MONOXIDE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)274,14214
Polymers271,0626
Non-polymers3,0818
Water29,0761614
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27670 Å2
ΔGint-199 kcal/mol
Surface area76470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.235, 193.884, 218.290
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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Protein , 3 types, 6 molecules ADBECF

#1: Protein CUTS, IRON-SULFUR PROTEIN OF CARBON MONOXIDE DEHYDROGENASE


Mass: 17747.441 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Hydrogenophaga pseudoflava (bacteria) / References: UniProt: P19915
#2: Protein CUTL, MOLYBDOPROTEIN OF CARBON MONOXIDE DEHYDROGENASE


Mass: 87345.383 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Hydrogenophaga pseudoflava (bacteria) / References: GenBank: 4098682, UniProt: P19913*PLUS
#3: Protein CUTM, FLAVOPROTEIN OF CARBON MONOXIDE DEHYDROGENASE


Mass: 30438.051 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Hydrogenophaga pseudoflava (bacteria) / References: UniProt: P19914

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Non-polymers , 4 types, 1622 molecules

#4: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#5: Chemical ChemComp-CDP / CYTIDINE-5'-DIPHOSPHATE / Cytidine diphosphate


Mass: 403.176 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N3O11P2
#6: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


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


Mass: 18.015 Da / Num. of mol.: 1614 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 63.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: potassium sodium tartrate, dihydrogen ammonium phosphate, methylpentanediol, dithioerythritol, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
135.5 mg/mlprotein1drop
250 mMHEPES-NaOH1drop
31.1 Msodium potassium tartrate1reservoir
40.3 Mammonium phosphate1reservoir
53 %(w/v)MPD1reservoir
610 mMDTE1reservoir

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→20 Å / Num. all: 570740 / Num. obs: 545063 / % possible obs: 91.1 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 4.7
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.366 / Num. unique all: 140414 / % possible all: 76.6
Reflection
*PLUS
Num. obs: 138188 / Num. measured all: 570740
Reflection shell
*PLUS
% possible obs: 76.6 %

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
RefinementResolution: 2.35→20 Å / σ(F): 2
RfactorNum. reflectionSelection details
Rfree0.245 4172 Random
Rwork0.208 --
all-140414 -
obs-134016 -
Refinement stepCycle: LAST / Resolution: 2.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22911 0 172 4842 27925
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0063
X-RAY DIFFRACTIONc_angle_deg1.63
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 3 % / Rfactor obs: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.35 Å / Lowest resolution: 2.43 Å / Rfactor Rfree: 0.322 / Rfactor obs: 0.33

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