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- PDB-3b9j: Structure of Xanthine Oxidase with 2-hydroxy-6-methylpurine -

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Basic information

Entry
Database: PDB / ID: 3b9j
TitleStructure of Xanthine Oxidase with 2-hydroxy-6-methylpurine
Components(xanthine oxidase) x 3
KeywordsOXIDOREDUCTASE / catalysis / intermediate / substrate orientation / peroxisome
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. / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / CO dehydrogenase flavoprotein, C-terminal domain / Aldehyde Oxidoreductase; domain 4 / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain / [2Fe-2S]-binding domain / CO dehydrogenase flavoprotein C-terminal domain / Molybdopterin dehydrogenase, FAD-binding ...Xanthine dehydrogenase, small subunit / Oxidoreductase, molybdopterin binding site / Eukaryotic molybdopterin oxidoreductases signature. / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / CO dehydrogenase flavoprotein, C-terminal domain / Aldehyde Oxidoreductase; domain 4 / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain / [2Fe-2S]-binding domain / 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 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD-binding, type PCMH, subdomain 1 / Aldehyde Oxidoreductase; domain 3 / 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. / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / 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 / Ubiquitin-like (UB roll) / DNA polymerase; domain 1 / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
6-methyl-3,9-dihydro-2H-purin-2-one / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / DIOXOTHIOMOLYBDENUM(VI) ION / Chem-MTE / Xanthine dehydrogenase/oxidase
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsPauff, J.M. / Zhang, J. / Bell, C.E. / Hille, R.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Substrate orientation in xanthine oxidase: crystal structure of enzyme in reaction with 2-hydroxy-6-methylpurine.
Authors: Pauff, J.M. / Zhang, J. / Bell, C.E. / Hille, R.
History
DepositionNov 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_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 oxidase
B: xanthine oxidase
C: xanthine oxidase
I: xanthine oxidase
J: xanthine oxidase
K: xanthine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)297,74019
Polymers294,0136
Non-polymers3,72713
Water15,511861
1
A: xanthine oxidase
B: xanthine oxidase
C: xanthine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,89010
Polymers147,0063
Non-polymers1,8847
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
I: xanthine oxidase
J: xanthine oxidase
K: xanthine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,8509
Polymers147,0063
Non-polymers1,8446
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)133.187, 73.794, 146.498
Angle α, β, γ (deg.)90.000, 98.870, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 3 types, 6 molecules AIBJCK

#1: Protein xanthine oxidase / E.C.1.17.3.2 / XO / Xanthine oxidoreductase


Mass: 24036.760 Da / Num. of mol.: 2 / Fragment: residues 1-219 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P80457, xanthine oxidase
#2: Protein xanthine oxidase / E.C.1.17.3.2 / XO / Xanthine oxidoreductase


Mass: 39005.188 Da / Num. of mol.: 2 / Fragment: residues 220-569 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P80457, xanthine oxidase
#3: Protein xanthine oxidase / E.C.1.17.3.2 / XO / Xanthine oxidoreductase


Mass: 83964.383 Da / Num. of mol.: 2 / Fragment: residues 570-1332 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P80457, xanthine oxidase

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Non-polymers , 7 types, 874 molecules

#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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: 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 / Source method: obtained synthetically / Formula: C10H14N5O6PS2
#8: Chemical ChemComp-MOS / DIOXOTHIOMOLYBDENUM(VI) ION


Mass: 161.012 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HMoO2S
#9: Chemical ChemComp-290 / 6-methyl-3,9-dihydro-2H-purin-2-one


Mass: 150.138 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6N4O
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 861 / 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: 2.42 Å3/Da / Density % sol: 49.16 %
Crystal growTemperature: 298 K / Method: batch / pH: 7
Details: PEG 8000, DTT, pyrophosphate, phosphate, TRIS, pH 7.0, batch, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→144.34 Å / Num. all: 120613 / Num. obs: 114520
Reflection shellResolution: 2.3→2.36 Å

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
Atdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FIQ

1fiq


Resolution: 2.3→144.34 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.889 / SU B: 8.088 / SU ML: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.345 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.263 6093 5.1 %RANDOM
Rwork0.194 ---
obs0.197 114520 96.25 %-
all-120613 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.698 Å2
Baniso -1Baniso -2Baniso -3
1--2.04 Å20 Å21.13 Å2
2---0.55 Å20 Å2
3---2.94 Å2
Refinement stepCycle: LAST / Resolution: 2.3→144.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18785 0 201 861 19847
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02219398
X-RAY DIFFRACTIONr_bond_other_d0.0010.0213164
X-RAY DIFFRACTIONr_angle_refined_deg1.7981.97426274
X-RAY DIFFRACTIONr_angle_other_deg1.078332131
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.91952432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.17223.811803
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.141153284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.78615114
X-RAY DIFFRACTIONr_chiral_restr0.1520.22954
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0221459
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023912
X-RAY DIFFRACTIONr_nbd_refined0.220.24216
X-RAY DIFFRACTIONr_nbd_other0.2120.213752
X-RAY DIFFRACTIONr_nbtor_refined0.1780.29138
X-RAY DIFFRACTIONr_nbtor_other0.0910.210151
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2220.2947
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0460.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3790.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2970.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3240.24
X-RAY DIFFRACTIONr_mcbond_it0.7431.512497
X-RAY DIFFRACTIONr_mcbond_other0.1431.54963
X-RAY DIFFRACTIONr_mcangle_it1.228219504
X-RAY DIFFRACTIONr_scbond_it1.87838002
X-RAY DIFFRACTIONr_scangle_it2.8884.56762
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 415 -
Rwork0.251 7910 -
all-8325 -
obs--90.53 %

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