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- PDB-3ax9: Bovine xanthine oxidase, protease cleaved form -

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Basic information

Entry
Database: PDB / ID: 3ax9
TitleBovine xanthine oxidase, protease cleaved form
ComponentsXanthine dehydrogenase/oxidase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


xanthine dehydrogenase complex / xanthine dehydrogenase / xanthine oxidase / xanthine oxidase activity / xanthine catabolic process / xanthine dehydrogenase activity / molybdenum ion binding / molybdopterin cofactor binding / FAD binding / 2 iron, 2 sulfur cluster binding ...xanthine dehydrogenase complex / xanthine dehydrogenase / xanthine oxidase / xanthine oxidase activity / xanthine catabolic process / xanthine dehydrogenase activity / molybdenum ion binding / molybdopterin cofactor binding / FAD binding / 2 iron, 2 sulfur cluster binding / peroxisome / flavin adenine dinucleotide binding / iron ion binding / protein homodimerization activity / extracellular space
Similarity search - Function
Xanthine dehydrogenase, small subunit / Oxidoreductase, molybdopterin binding site / Eukaryotic molybdopterin oxidoreductases signature. / CO dehydrogenase flavoprotein C-terminal 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/xanthine dehydrogenase ...Xanthine dehydrogenase, small subunit / Oxidoreductase, molybdopterin binding site / Eukaryotic molybdopterin oxidoreductases signature. / CO dehydrogenase flavoprotein C-terminal 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/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 / FAD-binding, type PCMH, subdomain 1 / 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. / 2Fe-2S iron-sulfur cluster binding domain / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / 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
Similarity search - Domain/homology
BICARBONATE ION / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / 2-HYDROXYBENZOIC ACID / Chem-XAX / Xanthine dehydrogenase/oxidase
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsIshikita, H. / Eger, B.T. / Pai, E.F. / Okamoto, K. / Nishino, T.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Protein conformational gating of enzymatic activity in xanthine oxidoreductase
Authors: Ishikita, H. / Eger, B.T. / Okamoto, K. / Nishino, T. / Pai, E.F.
History
DepositionMar 31, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Structure summary
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)298,30821
Polymers293,9862
Non-polymers4,32219
Water11,710650
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-11 kcal/mol
Surface area83370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.196, 72.966, 142.261
Angle α, β, γ (deg.)90.00, 98.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Xanthine dehydrogenase/oxidase / Xanthine dehydrogenase / XD / Xanthine oxidase / XO / Xanthine oxidoreductase


Mass: 146993.141 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)
References: UniProt: P80457, xanthine dehydrogenase, xanthine oxidase

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Non-polymers , 8 types, 669 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-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-XAX / {[(5aR,8R,9aR)-2-amino-4-oxo-6,7-di(sulfanyl-kappaS)-3,5,5a,8,9a,10-hexahydro-4H-pyrano[3,2-g]pteridin-8-yl]methyl dihydrogenato(2-) phosphate}(hydroxy)oxo(thioxo)molybdenum


Mass: 554.348 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13MoN5O8PS3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID


Mass: 138.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 650 / 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: 2.32 Å3/Da / Density % sol: 47.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.4
Details: 6-9% PEG 4000, 30% glycerol, 50mM potassium phosphate, 5mM DTT, 1mM salicylate, 0.2mM EDTA, pH 7.4, VAPOR DIFFUSION, temperature 293K

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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: Nov 28, 2010
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→38.13 Å / Num. all: 112876 / Num. obs: 118829

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Processing

SoftwareName: REFMAC / Version: 5.5.0110 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→38.13 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.881 / SU B: 8.335 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27902 5953 5 %RANDOM
Rwork0.21517 ---
obs0.21834 112876 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.603 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.3→38.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18909 0 238 650 19797
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02219551
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.711.97626466
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.58652437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.42723.791815
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.033153346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.97715118
X-RAY DIFFRACTIONr_chiral_restr0.1030.22961
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02114572
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6371.512132
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.186219562
X-RAY DIFFRACTIONr_scbond_it237419
X-RAY DIFFRACTIONr_scangle_it3.1824.56896
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.304→2.364 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 410 -
Rwork0.263 8003 -
obs--96.08 %

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