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- PDB-6ad4: Rat Xanthine oxidoreductase, D428A variant, NADH bound form -

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Basic information

Entry
Database: PDB / ID: 6ad4
TitleRat Xanthine oxidoreductase, D428A variant, NADH bound form
ComponentsXanthine dehydrogenase/oxidase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


Butyrophilin (BTN) family interactions / hypoxanthine catabolic process / hypoxanthine dehydrogenase activity / hypoxanthine oxidase activity / Azathioprine ADME / Purine catabolism / guanine catabolic process / deoxyguanosine catabolic process / xanthine dehydrogenase / xanthine oxidase ...Butyrophilin (BTN) family interactions / hypoxanthine catabolic process / hypoxanthine dehydrogenase activity / hypoxanthine oxidase activity / Azathioprine ADME / Purine catabolism / guanine catabolic process / deoxyguanosine catabolic process / xanthine dehydrogenase / xanthine oxidase / xanthine oxidase activity / xanthine catabolic process / xanthine dehydrogenase activity / GMP catabolic process / deoxyinosine catabolic process / deoxyadenosine catabolic process / dAMP catabolic process / inosine catabolic process / regulation of epithelial cell differentiation / response to azide / amide catabolic process / adenosine catabolic process / AMP catabolic process / dGMP catabolic process / response to aluminum ion / IMP catabolic process / allantoin metabolic process / response to carbon monoxide / molybdopterin cofactor binding / nitrite reductase (NO-forming) activity / iron-sulfur cluster assembly / cellular response to interleukin-1 / lactation / FAD binding / sarcoplasmic reticulum / response to hydrogen peroxide / 2 iron, 2 sulfur cluster binding / cellular response to tumor necrosis factor / peroxisome / flavin adenine dinucleotide binding / response to lipopolysaccharide / oxidoreductase activity / iron ion binding / 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 / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / URIC ACID / Xanthine dehydrogenase/oxidase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsOkamoto, K. / Kawaguchi, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)15H04702 Japan
CitationJournal: To Be Published
Title: Rat Xanthine oxidoreductase, D428A variant, NAD bound form
Authors: Okamoto, K. / Kawaguchi, Y.
History
DepositionJul 30, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 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: Xanthine dehydrogenase/oxidase
B: Xanthine dehydrogenase/oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)296,80414
Polymers292,7412
Non-polymers4,06412
Water24,2661347
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12570 Å2
ΔGint-122 kcal/mol
Surface area84830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.718, 138.334, 222.513
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 , 1 types, 2 molecules AB

#1: Protein Xanthine dehydrogenase/oxidase


Mass: 146370.344 Da / Num. of mol.: 2
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 , 6 types, 1359 molecules

#2: 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
#3: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3
#4: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#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-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1347 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsThe authors state this residue is Asp428Ala variant.

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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: 2.6 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 9-11% polyethylene glycol 8000, 0.6M Li2SO4, 5mM DTT, 1mM sodium salicylate, 0.4mM EDTA, 15% glycerol, 40mM HEPES (pH 6.20), VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→49.36 Å / Num. obs: 282210 / % possible obs: 99.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 21.8
Reflection shellResolution: 1.8→1.842 Å / Rmerge(I) obs: 0.215 / Num. unique obs: 26270

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AN1

3an1


Resolution: 1.8→49.36 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.087 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.101 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19829 8587 3 %RANDOM
Rwork0.16421 ---
obs0.16525 273512 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.373 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.8→49.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20016 0 242 1347 21605
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01420697
X-RAY DIFFRACTIONr_bond_other_d0.0020.01718759
X-RAY DIFFRACTIONr_angle_refined_deg1.731.67628036
X-RAY DIFFRACTIONr_angle_other_deg1.0471.63844048
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.04152586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9422.239996
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.982153542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.86915127
X-RAY DIFFRACTIONr_chiral_restr0.0880.22731
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0223093
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023751
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9861.99510358
X-RAY DIFFRACTIONr_mcbond_other1.9861.99410357
X-RAY DIFFRACTIONr_mcangle_it2.7322.98412938
X-RAY DIFFRACTIONr_mcangle_other2.7322.98412939
X-RAY DIFFRACTIONr_scbond_it2.822.31710339
X-RAY DIFFRACTIONr_scbond_other2.822.31710340
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1743.34815091
X-RAY DIFFRACTIONr_long_range_B_refined5.03823.84323069
X-RAY DIFFRACTIONr_long_range_B_other5.03823.84223070
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.795→1.842 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 606 -
Rwork0.201 19793 -
obs--98.49 %

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