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- PDB-4yty: Structure of rat xanthine oxidoreductase, C535A/C992R/C1324S, NAD... -

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Basic information

Entry
Database: PDB / ID: 4yty
TitleStructure of rat xanthine oxidoreductase, C535A/C992R/C1324S, NADH bound form
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 / 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 / AMP catabolic process / adenosine 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: 2.2 Å
AuthorsNishino, T. / Okamoto, K. / Kawaguchi, Y. / Matsumura, T. / Eger, B.T. / Pai, E.F.
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 18, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Feb 19, 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)297,18519
Polymers292,8412
Non-polymers4,34417
Water25,3471407
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13410 Å2
ΔGint-119 kcal/mol
Surface area85040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.988, 137.404, 222.705
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: 146420.281 Da / Num. of mol.: 2 / Mutation: C535A, C992R, C1324S
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 , 8 types, 1424 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-CA / CALCIUM ION


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


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


Mass: 168.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N4O3
#6: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3
#7: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1407 / 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: 2.64 Å3/Da / Density % sol: 53.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
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: Dec 9, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→49.5 Å / Num. obs: 153088 / % possible obs: 99.7 % / Redundancy: 7.4 % / Net I/σ(I): 18.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.2.0019refinement
PDB_EXTRACT3.15data extraction
SCALEPACKdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AN1

3an1


Resolution: 2.2→49.5 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.579 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.243 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2211 7678 5 %RANDOM
Rwork0.1778 ---
obs0.18 145410 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 192.89 Å2 / Biso mean: 21.237 Å2 / Biso min: 5.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.2→49.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20071 0 256 1407 21734
Biso mean--19.63 26.2 -
Num. residues----2597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02220762
X-RAY DIFFRACTIONr_angle_refined_deg1.2941.98128121
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.09252593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.40424.016874
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.121153550
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.89815129
X-RAY DIFFRACTIONr_chiral_restr0.0870.23150
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215539
X-RAY DIFFRACTIONr_nbd_refined0.1920.29398
X-RAY DIFFRACTIONr_nbtor_refined0.2990.214176
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.21484
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.212
X-RAY DIFFRACTIONr_mcbond_it0.6431.513363
X-RAY DIFFRACTIONr_mcangle_it1.033220865
X-RAY DIFFRACTIONr_scbond_it1.59238506
X-RAY DIFFRACTIONr_scangle_it2.5674.57248
LS refinement shellResolution: 2.203→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 561 -
Rwork0.187 10212 -
all-10773 -
obs--96.02 %

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