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- PDB-3etr: Crystal structure of xanthine oxidase in complex with lumazine -

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Basic information

Entry
Database: PDB / ID: 3etr
TitleCrystal structure of xanthine oxidase in complex with lumazine
Components(Xanthine dehydrogenase/oxidase) x 3
KeywordsOXIDOREDUCTASE / protein-ligand complex / enzyme catalysis / substrate orientation / FAD / Flavoprotein / Iron / Iron-sulfur / Metal-binding / Molybdenum / NAD / 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 / CO dehydrogenase flavoprotein C-terminal domain / Aldehyde Oxidoreductase; domain 4 / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain / [2Fe-2S]-binding 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 / CO dehydrogenase flavoprotein C-terminal domain / Aldehyde Oxidoreductase; domain 4 / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain / [2Fe-2S]-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 / Aldehyde oxidase/xanthine dehydrogenase / Aldehyde oxidase/xanthine dehydrogenase, second molybdopterin binding domain / Molybdopterin cofactor-binding domain / 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 / [2Fe-2S] 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 / FAD-binding, type PCMH, subdomain 2 / 2Fe-2S iron-sulfur cluster binding domain / FAD-binding, type PCMH-like superfamily / Beta-grasp domain superfamily / Enolase-like; domain 1 / 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
FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / pteridine-2,4(1H,3H)-dione / DIOXOTHIOMOLYBDENUM(VI) ION / Chem-MTE / Xanthine dehydrogenase/oxidase
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsPauff, J.M. / Cao, H. / Hille, R.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Substrate Orientation and Catalysis at the Molybdenum Site in Xanthine Oxidase: CRYSTAL STRUCTURES IN COMPLEX WITH XANTHINE AND LUMAZINE.
Authors: Pauff, J.M. / Cao, H. / Hille, R.
History
DepositionOct 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 10, 2014Group: Database references
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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 dehydrogenase/oxidase
B: Xanthine dehydrogenase/oxidase
C: Xanthine dehydrogenase/oxidase
L: Xanthine dehydrogenase/oxidase
M: Xanthine dehydrogenase/oxidase
N: Xanthine dehydrogenase/oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)273,74319
Polymers269,9876
Non-polymers3,75513
Water22,1941232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24080 Å2
ΔGint-83.2 kcal/mol
Surface area81930 Å2
MethodPISA
2
A: Xanthine dehydrogenase/oxidase
B: Xanthine dehydrogenase/oxidase
C: Xanthine dehydrogenase/oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,89110
Polymers134,9943
Non-polymers1,8987
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8930 Å2
ΔGint-37.4 kcal/mol
Surface area43820 Å2
MethodPISA
3
L: Xanthine dehydrogenase/oxidase
M: Xanthine dehydrogenase/oxidase
N: Xanthine dehydrogenase/oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,8519
Polymers134,9943
Non-polymers1,8586
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9210 Å2
ΔGint-38.6 kcal/mol
Surface area44050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.190, 73.491, 146.505
Angle α, β, γ (deg.)90.000, 98.680, 90.000
Int Tables number4
Space group name H-MP1211
DetailsBIOLOGICAL UNIT IS THE SAME AS ASYMMETRIC UNIT.

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Components

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Protein , 3 types, 6 molecules ALBMCN

#1: Protein Xanthine dehydrogenase/oxidase / [Includes: Xanthine dehydrogenase (EC 1.17.1.4) (XD) / and Xanthine oxidase (EC 1.17.3.2) (XO) ...[Includes: Xanthine dehydrogenase (EC 1.17.1.4) (XD) / and Xanthine oxidase (EC 1.17.3.2) (XO) (Xanthine oxidoreductase)]


Mass: 18002.881 Da / Num. of mol.: 2 / Fragment: UNP residues 2-165 / Source method: isolated from a natural source / Details: Animal Milk / Source: (natural) Bos taurus (cattle) / References: UniProt: P80457
#2: Protein Xanthine dehydrogenase/oxidase


Mass: 34024.590 Da / Num. of mol.: 2 / Fragment: UNP residues 224-528 / Source method: isolated from a natural source / Details: Animal Milk / Source: (natural) Bos taurus (cattle) / References: UniProt: P80457
#3: Protein Xanthine dehydrogenase/oxidase


Mass: 82966.203 Da / Num. of mol.: 2 / Fragment: UNP residues 571-1325 / Source method: isolated from a natural source / Details: Animal Milk / Source: (natural) Bos taurus (cattle) / References: UniProt: P80457

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Non-polymers , 7 types, 1245 molecules

#4: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#5: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#6: 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
#7: Chemical ChemComp-MOS / DIOXOTHIOMOLYBDENUM(VI) ION


Mass: 161.012 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HMoO2S
#8: Chemical ChemComp-LUZ / pteridine-2,4(1H,3H)-dione / Lumazine / 2,4-dihydroxypteridine / 2,4-pteridinediol


Mass: 164.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H4N4O2
#9: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1232 / 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: 2.63 Å3/Da / Density % sol: 53.15 %
Crystal growTemperature: 298 K / Method: batch / pH: 7.2 / Details: PEG 8000, pH 7.2, 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: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 15, 2007 / Details: APS BEAMLINE SGX PHARMACEUTICALS
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 140747 / % possible obs: 98.7 % / Biso Wilson estimate: 13.1 Å2 / Rsym value: 0.197 / Net I/σ(I): 5
Reflection shellResolution: 2.2→2.257 Å / % possible obs: 96.1 % / Mean I/σ(I) obs: 1.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.11 Å26.42 Å
Translation2.11 Å26.42 Å

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FIQ

1fiq


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.893 / WRfactor Rfree: 0.283 / WRfactor Rwork: 0.209 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.803 / SU B: 6.927 / SU ML: 0.176 / SU R Cruickshank DPI: 0.276 / SU Rfree: 0.234 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.276 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.267 7052 5 %RANDOM
Rwork0.197 ---
obs0.201 140747 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.91 Å2 / Biso mean: 29.464 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--2.54 Å20 Å21.16 Å2
2--0.08 Å20 Å2
3---2.81 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18872 0 203 1232 20307
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02219485
X-RAY DIFFRACTIONr_angle_refined_deg1.961.97426377
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.96752432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.12123.791815
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.192153337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.31815118
X-RAY DIFFRACTIONr_chiral_restr0.1290.22953
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214540
X-RAY DIFFRACTIONr_nbd_refined0.2380.29387
X-RAY DIFFRACTIONr_nbtor_refined0.3080.213095
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.21322
X-RAY DIFFRACTIONr_metal_ion_refined0.6110.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2630.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.290.23
X-RAY DIFFRACTIONr_mcbond_it1.0011.512489
X-RAY DIFFRACTIONr_mcangle_it1.609219520
X-RAY DIFFRACTIONr_scbond_it2.66438105
X-RAY DIFFRACTIONr_scangle_it4.0074.56849
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 496 -
Rwork0.236 9645 -
all-10141 -
obs--96.11 %

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