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- PDB-1fo4: CRYSTAL STRUCTURE OF XANTHINE DEHYDROGENASE ISOLATED FROM BOVINE MILK -

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Entry
Database: PDB / ID: 1fo4
TitleCRYSTAL STRUCTURE OF XANTHINE DEHYDROGENASE ISOLATED FROM BOVINE MILK
ComponentsXANTHINE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / Xanthine Dehydrogenase / FAD / molybdopterin / 2Fe-2S iron sulfur centers / salicylate
Function / homology2Fe-2S ferredoxin, iron-sulphur binding site / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead superfamily / Aldehyde oxidase/xanthine dehydrogenase / FAD-binding domain, PCMH-type / Xanthine dehydrogenase, small subunit / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding / FAD-binding, type PCMH-like superfamily / CO dehydrogenase flavoprotein, C-terminal / [2Fe-2S]-binding / Molybdopterin dehydrogenase, FAD-binding ...2Fe-2S ferredoxin, iron-sulphur binding site / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead superfamily / Aldehyde oxidase/xanthine dehydrogenase / FAD-binding domain, PCMH-type / Xanthine dehydrogenase, small subunit / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding / FAD-binding, type PCMH-like superfamily / CO dehydrogenase flavoprotein, C-terminal / [2Fe-2S]-binding / Molybdopterin dehydrogenase, FAD-binding / 2Fe-2S ferredoxin-type iron-sulfur binding domain / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / CO dehydrogenase flavoprotein, C-terminal domain superfamily / [2Fe-2S]-binding domain superfamily / 2Fe-2S ferredoxin-like superfamily / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain superfamily / 2Fe-2S iron-sulfur cluster binding domain / FAD binding domain in molybdopterin dehydrogenase / 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 region signature. / Eukaryotic molybdopterin oxidoreductases signature. / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / PCMH-type FAD-binding domain profile. / Oxidoreductase, molybdopterin binding site / xanthine dehydrogenase complex / xanthine dehydrogenase / xanthine oxidase / xanthine catabolic process / xanthine oxidase activity / xanthine dehydrogenase activity / molybdopterin cofactor binding / molybdenum ion binding / FAD binding / 2 iron, 2 sulfur cluster binding / peroxisome / flavin adenine dinucleotide binding / electron transfer activity / iron ion binding / protein homodimerization activity / extracellular space / cytosol / Xanthine dehydrogenase/oxidase
Function and homology information
Specimen sourceBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 2.1 Å resolution
AuthorsEnroth, C. / Eger, B.T. / Okamoto, K. / Nishino, T. / Nishino, T. / Pai, E.F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Crystal structures of bovine milk xanthine dehydrogenase and xanthine oxidase: structure-based mechanism of conversion.
Authors: Enroth, C. / Eger, B.T. / Okamoto, K. / Nishino, T. / Nishino, T. / Pai, E.F.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 24, 2000 / Release: Oct 25, 2000
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 25, 2000Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelNon-polymer description / Version format compliance
1.3Feb 1, 2017Structure modelStructure summary
1.4Oct 4, 2017Structure modelRefinement descriptionsoftware_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: XANTHINE DEHYDROGENASE
B: XANTHINE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)298,09820
Polyers293,9862
Non-polymers4,11218
Water36,8772047
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)13540
ΔGint (kcal/M)-123
Surface area (Å2)87860
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)169.451, 124.493, 148.327
Angle α, β, γ (deg.)90.000, 90.940, 90.000
Int Tables number5
Space group name H-MC 1 2 1
DetailsThe biological assmbly is a dimer constructed from a single chain in each biological monomer. The monomer is divided into 3 chains due to 2 missing loops of electron density. The dimer is generated by a two-fold.

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Components

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Protein/peptide , 1 types, 2 molecules AB

#1: Protein/peptide XANTHINE DEHYDROGENASE / / XD


Mass: 146993.141 Da / Num. of mol.: 2 / Source: (natural) Bos taurus (cattle) / Genus: Bos / Secretion: MILK / References: UniProt: P80457, 1.1.1.204

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Non-polymers , 8 types, 2065 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Formula: Ca / Calcium
#3: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Formula: Fe2S2
#4: Chemical ChemComp-MTE / PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER


Mass: 395.352 Da / Num. of mol.: 2 / Formula: C10H14N5O6PS2
#5: Chemical ChemComp-MOS / DIOXOTHIOMOLYBDENUM(VI) ION


Mass: 161.012 Da / Num. of mol.: 2 / Formula: HMoO2S
#6: Chemical ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID


Mass: 138.121 Da / Num. of mol.: 2 / Formula: C7H6O3 / Salicylic acid
#7: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Formula: C27H33N9O15P2 / Flavin adenine dinucleotide / Comment: FAD *YM
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Formula: C3H8O3 / Glycerol
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2047 / 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: 2.66 / Density percent sol: 53.75 %
Crystal growTemp: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 4000, DTT, glycerol, KPi, NaPPi, salicylate, EDTA, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K
Crystal grow
*PLUS
Method: unknown / Details: unpublished data

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Data collection

DiffractionMean temperature: 1 kelvins
SourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.97895
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Collection date: Feb 7, 1999
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 14.2 Å2 / D resolution high: 2.1 Å / D resolution low: 24.9 Å / Number all: 176889 / Number obs: 154198 / Observed criterion sigma F: 0 / Observed criterion sigma I: -3 / Rmerge I obs: 0.095 / NetI over sigmaI: 11.9 / Redundancy: 2.8 % / Percent possible obs: 87.2
Reflection shellRmerge I obs: 0.387 / Highest resolution: 2.1 Å / Lowest resolution: 2.14 Å / Number unique all: 5988 / Redundancy: 2.1 % / Percent possible all: 67.8
Reflection
*PLUS
Number obs: 7710 / Number measured all: 154198
Reflection shell
*PLUS
Percent possible obs: 67.8

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Processing

Software
NameClassification
SOLVEphasing
SHARPphasing
EPMRphasing
SIGMAAmodel building
DMmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
SIGMAAphasing
DMphasing
CNSphasing
RefineR Free selection details: RANDOM / Sigma F: 0 / Sigma I: 0 / Stereochemistry target values: Engh & Huber
Least-squares processR factor R free: 0.238 / R factor R work: 0.198 / Highest resolution: 2.1 Å / Lowest resolution: 25 Å / Number reflection R free: 7710 / Number reflection all: 179008 / Number reflection obs: 154198 / Percent reflection obs: 86.9
Refine hist #LASTHighest resolution: 2.1 Å / Lowest resolution: 25 Å
Number of atoms included #LASTProtein: 20131 / Nucleic acid: 0 / Ligand: 224 / Solvent: 2047 / Total: 22402
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.010
X-RAY DIFFRACTIONc_angle_deg1.4
Software
*PLUS
Name: CNS / Classification: refinement
Displacement parameters
*PLUS
B iso mean: 18.8 Å2

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