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- PDB-4yrw: rat xanthine oxidoreductase, C-terminal deletion protein variant -

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Basic information

Entry
Database: PDB / ID: 4yrw
Titlerat xanthine oxidoreductase, C-terminal deletion protein variant
ComponentsXanthine dehydrogenase/oxidase
KeywordsOXIDOREDUCTASE / xanthine oxidoreductase / xanthine oxidase / xanthine dehydrogenase / D/O conversion
Function / homology
Function and homology information


Butyrophilin (BTN) family interactions / hypoxanthine catabolic process / hypoxanthine dehydrogenase activity / hypoxanthine oxidase activity / negative regulation of vasculogenesis / Azathioprine ADME / Purine catabolism / guanine catabolic process / deoxyguanosine catabolic process / dGMP catabolic process ...Butyrophilin (BTN) family interactions / hypoxanthine catabolic process / hypoxanthine dehydrogenase activity / hypoxanthine oxidase activity / negative regulation of vasculogenesis / Azathioprine ADME / Purine catabolism / guanine catabolic process / deoxyguanosine catabolic process / dGMP catabolic process / xanthine dehydrogenase / xanthine oxidase / xanthine oxidase activity / xanthine catabolic process / xanthine dehydrogenase activity / GMP catabolic process / amide catabolic process / negative regulation of endothelial cell differentiation / deoxyinosine catabolic process / deoxyadenosine catabolic process / regulation of epithelial cell differentiation / dAMP catabolic process / inosine catabolic process / negative regulation of vascular endothelial growth factor signaling pathway / adenosine catabolic process / response to carbon monoxide / response to azide / AMP catabolic process / IMP catabolic process / allantoin metabolic process / response to aluminum ion / molybdopterin cofactor binding / positive regulation of p38MAPK cascade / nitrite reductase (NO-forming) activity / iron-sulfur cluster assembly / negative regulation of endothelial cell proliferation / cellular response to interleukin-1 / lactation / FAD binding / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / sarcoplasmic reticulum / response to hydrogen peroxide / 2 iron, 2 sulfur cluster binding / positive regulation of reactive oxygen species metabolic process / peroxisome / cellular response to tumor necrosis factor / flavin adenine dinucleotide binding / response to lipopolysaccharide / oxidoreductase activity / iron ion binding / negative regulation of gene expression / protein homodimerization activity / extracellular space / identical protein binding / cytosol
Similarity search - Function
Xanthine dehydrogenase, small subunit / Oxidoreductase, molybdopterin binding site / Eukaryotic molybdopterin oxidoreductases signature. / 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 ...Xanthine dehydrogenase, small subunit / Oxidoreductase, molybdopterin binding site / Eukaryotic molybdopterin oxidoreductases signature. / 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 / Aldehyde Oxidoreductase; domain 3 / FAD-binding, type PCMH, subdomain 1 / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 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
BICARBONATE ION / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / URIC ACID / Xanthine dehydrogenase/oxidase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsOkamoto, K.
CitationJournal: Febs J. / Year: 2015
Title: The C-terminal peptide plays a role in the formation of an intermediate form during the transition between xanthine dehydrogenase and xanthine oxidase
Authors: Nishino, T. / Okamoto, K. / Kawaguchi, Y. / Matsumura, T. / Eger, B.T. / Pai, E.F. / Nishino, T.
History
DepositionMar 16, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Feb 5, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 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: Xanthine dehydrogenase/oxidase
B: Xanthine dehydrogenase/oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)292,39417
Polymers289,3052
Non-polymers3,08915
Water11,494638
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10840 Å2
ΔGint-108 kcal/mol
Surface area85350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.497, 138.468, 222.213
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Xanthine dehydrogenase/oxidase


Mass: 144652.344 Da / Num. of mol.: 2 / Fragment: UNP residues 1-1314
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Xdh / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P22985, xanthine dehydrogenase, xanthine oxidase

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Non-polymers , 7 types, 653 molecules

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


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#6: Chemical ChemComp-URC / URIC ACID / 7,9-DIHYDRO-1H-PURINE-2,6,8(3H)-TRIONE


Mass: 168.110 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4N4O3
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 638 / 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: 2.67 Å3/Da / Density % sol: 53.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG 8000, lithium formate, DTT, sodium salicylate, EDTA, glycerol, HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 19, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 206697 / % possible obs: 99.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Χ2: 1.015 / Net I/av σ(I): 22.286 / Net I/σ(I): 15.1 / Num. measured all: 767890
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.99-2.063.60.202198480.96696.4
2.06-2.143.70.167205511.04999.9
2.14-2.243.70.138206290.995100
2.24-2.363.70.122206171.035100
2.36-2.513.80.102206150.969100
2.51-2.73.80.085207150.953100
2.7-2.973.80.073207571.069100
2.97-3.43.80.061208171.034100
3.4-4.293.70.049209501.088100
4.29-503.70.036211980.98698.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
SCALEPACKdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WYG

1wyg


Resolution: 1.99→43.33 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.607 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2293 10396 5 %RANDOM
Rwork0.1861 ---
obs0.1883 196212 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 108.23 Å2 / Biso mean: 29.599 Å2 / Biso min: 13.01 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2---0 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.99→43.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19904 0 174 638 20716
Biso mean--25.92 24.92 -
Num. residues----2575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.01920503
X-RAY DIFFRACTIONr_bond_other_d0.0020.0219606
X-RAY DIFFRACTIONr_angle_refined_deg2.0681.97727758
X-RAY DIFFRACTIONr_angle_other_deg0.98345255
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8352571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.36324.048867
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.18153523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.80315126
X-RAY DIFFRACTIONr_chiral_restr0.1510.23104
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02123061
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024563
X-RAY DIFFRACTIONr_mcbond_it2.6412.75110296
X-RAY DIFFRACTIONr_mcbond_other2.642.75110295
X-RAY DIFFRACTIONr_mcangle_it3.4854.1112863
LS refinement shellResolution: 1.992→2.043 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 765 -
Rwork0.221 14034 -
all-14799 -
obs--97.33 %

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