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- PDB-1ffv: CARBON MONOXIDE DEHYDROGENASE FROM HYDROGENOPHAGA PSEUDOFLAVA -

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Basic information

Entry
Database: PDB / ID: 1ffv
TitleCARBON MONOXIDE DEHYDROGENASE FROM HYDROGENOPHAGA PSEUDOFLAVA
Components
  • CUTL, MOLYBDOPROTEIN OF CARBON MONOXIDE DEHYDROGENASE
  • CUTM, FLAVOPROTEIN OF CARBON MONOXIDE DEHYDROGENASE
  • CUTS, IRON-SULFUR PROTEIN OF CARBON MONOXIDE DEHYDROGENASE
KeywordsHYDROLASE / DEHYDROGENASE
Function / homologyFAD-binding, type PCMH, subdomain 2 / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding / [2Fe-2S]-binding domain superfamily / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead superfamily / CO dehydrogenase flavoprotein, C-terminal domain superfamily / FAD-binding, type PCMH-like superfamily / 2Fe-2S ferredoxin-like superfamily / FAD binding domain in molybdopterin dehydrogenase / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type ...FAD-binding, type PCMH, subdomain 2 / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding / [2Fe-2S]-binding domain superfamily / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead superfamily / CO dehydrogenase flavoprotein, C-terminal domain superfamily / FAD-binding, type PCMH-like superfamily / 2Fe-2S ferredoxin-like superfamily / FAD binding domain in molybdopterin dehydrogenase / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / Carbon-monoxide dehydrogenase, large subunit / Beta-grasp domain superfamily / CO dehydrogenase flavoprotein, C-terminal / 2Fe-2S iron-sulfur cluster binding domain / [2Fe-2S]-binding / Molybdopterin dehydrogenase, FAD-binding / 2Fe-2S ferredoxin-type iron-sulfur binding domain / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain / [2Fe-2S] binding domain / Molybdopterin-binding domain of aldehyde dehydrogenase / CO dehydrogenase flavoprotein C-terminal domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / PCMH-type FAD-binding domain profile. / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain superfamily / aerobic carbon monoxide dehydrogenase / carbon-monoxide dehydrogenase (acceptor) activity / molybdenum ion binding / FAD binding / 2 iron, 2 sulfur cluster binding / copper ion binding / electron transfer activity / metal ion binding / Carbon monoxide dehydrogenase large chain / Carbon monoxide dehydrogenase medium chain / Carbon monoxide dehydrogenase small chain / gb:4098682:
Function and homology information
Specimen sourceHydrogenophaga pseudoflava (bacteria)
MethodX-RAY DIFFRACTION / 2.25 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 26, 2000 / Release: Sep 15, 2000
RevisionDateData content typeGroupProviderType
1.0Sep 15, 2000Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)275,25314
Polyers271,2906
Non-polymers3,9638
Water28,9501607
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)28810
ΔGint (kcal/M)-195
Surface area (Å2)76340
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)86.373, 193.793, 218.755
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

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Components

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Protein/peptide , 3 types, 6 molecules ADBECF

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


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


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


Mass: 30552.148 Da / Num. of mol.: 2 / Source: (natural) Hydrogenophaga pseudoflava (bacteria) / Genus: Hydrogenophaga / References: UniProt: P19914

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Non-polymers , 4 types, 1615 molecules

#4: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Formula: Fe2S2
#5: Chemical ChemComp-PCD / (MOLYBDOPTERIN-CYTOSINE DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V) / MOLYBDENUM COFACTOR / MOCO


Mass: 844.471 Da / Num. of mol.: 2 / Formula: C19H26MoN8O16P2S2 / Molybdenum cofactor
#6: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Formula: C27H33N9O15P2 / Flavin adenine dinucleotide / Comment: FAD *YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1607 / Formula: H2O / Water

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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: 3.37 / Density percent sol: 63.53 %
Crystal growTemp: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: potassium sodium tartrate, dihydrogen ammonium phosphate, methylpentandediol, dithioerythritol, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temp: 4 K
components of the solutions
*PLUS
IDConcCommon 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 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionD resolution high: 2.25 Å / D resolution low: 20 Å / Number all: 433970 / Number obs: 407833 / Observed criterion sigma I: 2 / Rmerge I obs: 0.083 / NetI over sigmaI: 7.7 / Redundancy: 2.6 % / Percent possible obs: 94
Reflection shellRmerge I obs: 0.358 / Highest resolution: 2.25 Å / Lowest resolution: 2.32 Å / Number unique all: 165339 / Redundancy: 2.6 % / Percent possible all: 79.7
Reflection
*PLUS
Number obs: 162740 / Number measured all: 433970
Reflection shell
*PLUS
Percent possible obs: 79.7

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
RefineR Free selection details: Random / Sigma F: 2
Least-squares processR factor R free: 0.237 / R factor R work: 0.209 / Highest resolution: 2.25 Å / Lowest resolution: 20 Å / Number reflection R free: 8090 / Number reflection all: 165339 / Number reflection obs: 154650
Refine hist #LASTHighest resolution: 2.25 Å / Lowest resolution: 20 Å
Number of atoms included #LASTProtein: 22926 / Nucleic acid: 0 / Ligand: 218 / Solvent: 4821 / Total: 27965
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d1.72
X-RAY DIFFRACTIONc_angle_deg0.0073
Software
*PLUS
Name: CNS / Classification: refinement
Refine
*PLUS
Sigma F: 2
Least-squares process
*PLUS
R factor obs: 0.209 / Lowest resolution: 2 Å / Percent reflection R free: 5
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0073
X-RAY DIFFRACTIONc_angle_deg1.72
Refine LS shell
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 2.32 Å / R factor obs: 0.323 / R factor R free: 0.341

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