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- PDB-5y6q: Crystal structure of an aldehyde oxidase from Methylobacillus sp.... -

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Basic information

Entry
Database: PDB / ID: 5y6q
TitleCrystal structure of an aldehyde oxidase from Methylobacillus sp. KY4400
Components(Aldehyde oxidase ...) x 3
KeywordsOXIDOREDUCTASE / aldehyde oxidase molybdenum enzyme Methylobacillus sp. KY4400
Function / homology
Function and homology information


FAD binding / 2 iron, 2 sulfur cluster binding / electron transfer activity / oxidoreductase activity / metal ion binding
Similarity search - Function
CO dehydrogenase flavoprotein, C-terminal domain / CO dehydrogenase flavoprotein C-terminal 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 and xanthine dehydrogenase, a/b hammerhead domain / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead ...CO dehydrogenase flavoprotein, C-terminal domain / CO dehydrogenase flavoprotein C-terminal 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 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 / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / Beta-grasp domain / FAD-binding, type PCMH, subdomain 2 / 2Fe-2S iron-sulfur cluster binding domain / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / ISOPROPYL ALCOHOL / PTERIN CYTOSINE DINUCLEOTIDE / DIOXOTHIOMOLYBDENUM(VI) ION / IRON/SULFUR CLUSTER / Aldehyde oxidase large subunit / Aldehyde oxidase medium subunit / Aldehyde oxidase small subunit
Similarity search - Component
Biological speciesMethylobacillus sp. KY4400 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMikami, B. / Uchida, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan
Citation
Journal: J. Biochem. / Year: 2018
Title: Crystal structure of an aldehyde oxidase from Methylobacillus sp. KY4400.
Authors: Uchida, H. / Mikami, B. / Yamane-Tanabe, A. / Ito, A. / Hirano, K. / Oki, M.
#1: Journal: Biosci. Biotechnol. Biochem. / Year: 2005
Title: Cloning and sequencing of the aldehyde oxidase gene from Methylobacillus sp. KY4400.
Authors: Yasuhara, A. / Akiba-Goto, M. / Aisaka, K.
History
DepositionAug 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldehyde oxidase small subunit
B: Aldehyde oxidase medium subunit
C: Aldehyde oxidase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,25329
Polymers136,0823
Non-polymers4,17226
Water9,134507
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17110 Å2
ΔGint-235 kcal/mol
Surface area39710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.972, 77.972, 400.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Aldehyde oxidase ... , 3 types, 3 molecules ABC

#1: Protein Aldehyde oxidase small subunit /


Mass: 17311.635 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylobacillus sp. KY4400 (bacteria) / Gene: aoms / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q84IY0
#2: Protein Aldehyde oxidase medium subunit


Mass: 35616.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylobacillus sp. KY4400 (bacteria) / Gene: aomm / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q84IX9
#3: Protein Aldehyde oxidase large subunit /


Mass: 83153.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylobacillus sp. KY4400 (bacteria) / Gene: aoml / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q84IX8

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Non-polymers , 9 types, 533 molecules

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


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#7: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-MOS / DIOXOTHIOMOLYBDENUM(VI) ION


Mass: 161.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HMoO2S
#10: Chemical ChemComp-MCN / PTERIN CYTOSINE DINUCLEOTIDE


Mass: 696.501 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22N8O13P2S2
#11: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 507 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsThe depositors state that the database UNP codes Q84IY0/Q84IX9 are incorrect at these positions.

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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 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Sodium citrate buffer, pH 5.5, 4-5% W/V isopropanol, 22-27% W/V PEG 4000, 10-16% W/V ammonium sulfate, red cubic flash cooled after brief soaking to the bottom solution containing 30% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 8, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 44006 / % possible obs: 99.1 % / Redundancy: 15.1 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.022 / Χ2: 0.856 / Net I/σ(I): 24.5
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 3.13 / Num. unique obs: 1944 / CC1/2: 0.901 / Rpim(I) all: 0.161 / Χ2: 0.487 / % possible all: 90.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
DENZO706data reduction
SCALEPACK706data scaling
MOLREP11.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5G5H

5g5h


Resolution: 2.5→46.116 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2332 2210 5.04 %
Rwork0.1778 --
obs0.1806 43878 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→46.116 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9310 0 221 507 10038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059715
X-RAY DIFFRACTIONf_angle_d0.81413199
X-RAY DIFFRACTIONf_dihedral_angle_d16.4855809
X-RAY DIFFRACTIONf_chiral_restr0.0531473
X-RAY DIFFRACTIONf_plane_restr0.0051721
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4998-2.55410.33911180.23132346X-RAY DIFFRACTION91
2.5541-2.61360.28611230.21472478X-RAY DIFFRACTION95
2.6136-2.67890.27781460.20312544X-RAY DIFFRACTION99
2.6789-2.75130.27571230.20572557X-RAY DIFFRACTION100
2.7513-2.83230.27671320.21022573X-RAY DIFFRACTION100
2.8323-2.92370.26361220.20332597X-RAY DIFFRACTION100
2.9237-3.02820.26831550.20192566X-RAY DIFFRACTION100
3.0282-3.14940.28251430.20872591X-RAY DIFFRACTION100
3.1494-3.29270.23931380.19712596X-RAY DIFFRACTION100
3.2927-3.46620.25551370.17912610X-RAY DIFFRACTION100
3.4662-3.68330.241530.16712617X-RAY DIFFRACTION100
3.6833-3.96750.20261500.16072619X-RAY DIFFRACTION100
3.9675-4.36650.1861390.14412650X-RAY DIFFRACTION100
4.3665-4.99770.17491240.14422695X-RAY DIFFRACTION100
4.9977-6.29410.20531490.17012706X-RAY DIFFRACTION100
6.2941-46.12390.19911580.16172923X-RAY DIFFRACTION100

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