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- PDB-1fiq: CRYSTAL STRUCTURE OF XANTHINE OXIDASE FROM BOVINE MILK -

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Basic information

Entry
Database: PDB / ID: 1fiq
TitleCRYSTAL STRUCTURE OF XANTHINE OXIDASE FROM BOVINE MILK
Components(XANTHINE OXIDASE) x 3
KeywordsOXIDOREDUCTASE / Xanthine Oxidase
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. / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain / FAD-binding, type PCMH, subdomain 2 / 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 / DIOXOTHIOMOLYBDENUM(VI) ION / Chem-MTE / 2-HYDROXYBENZOIC ACID / Xanthine dehydrogenase/oxidase
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsEnroth, C. / Eger, B.T. / Okamoto, K. / Nishino, T. / Nishino, T. / Pai, E.F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Crystal structures of bovine milk xanthine dehydrogenase and xanthine oxidase: structure-based mechanism of conversion.
Authors: Enroth, C. / Eger, B.T. / Okamoto, K. / Nishino, T. / Nishino, T. / Pai, E.F.
History
DepositionAug 4, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Feb 7, 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_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_conn.ptnr2_label_seq_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,95310
Polymers147,0293
Non-polymers1,9247
Water10,737596
1
A: XANTHINE OXIDASE
B: XANTHINE OXIDASE
C: XANTHINE OXIDASE
hetero molecules

A: XANTHINE OXIDASE
B: XANTHINE OXIDASE
C: XANTHINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)297,90620
Polymers294,0596
Non-polymers3,84814
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+3/21
Buried area30920 Å2
ΔGint-188 kcal/mol
Surface area80480 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)117.831, 165.403, 154.447
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein XANTHINE OXIDASE / / XO


Mass: 24036.760 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-219 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Secretion: MILK / References: UniProt: P80457, EC: 1.1.3.22
#2: Protein XANTHINE OXIDASE / / XO


Mass: 39028.246 Da / Num. of mol.: 1 / Fragment: RESIDUES 220-569 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Secretion: MILK / References: UniProt: P80457, EC: 1.1.3.22
#3: Protein XANTHINE OXIDASE / / XO


Mass: 83964.383 Da / Num. of mol.: 1 / Fragment: RESIDUES 570-1332 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Secretion: MILK / References: UniProt: P80457, EC: 1.1.3.22

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Non-polymers , 7 types, 603 molecules

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


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#5: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: C10H14N5O6PS2
#7: Chemical ChemComp-MOS / DIOXOTHIOMOLYBDENUM(VI) ION


Mass: 161.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HMoO2S
#8: Chemical ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID / Salicylic acid


Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O3
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 596 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.91 %
Crystal grow
*PLUS
Method: unknown / Details: unpublished data

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B
DetectorType: ADSC / Detector: CCD / Date: Apr 25, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→30 Å / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 37.1 Å2 / Net I/σ(I): 16.5
Reflection shellResolution: 2.5→2.59 Å / Mean I/σ(I) obs: 3.35 / % possible all: 97.5
Reflection
*PLUS
Num. obs: 51300
Reflection shell
*PLUS
% possible obs: 97.5 %

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Processing

Software
NameVersionClassification
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.5→8 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2993012.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.275 2459 5 %RANDOM
Rwork0.212 ---
obs0.212 49668 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 71.7 Å2 / ksol: 0.3761 e/Å3
Displacement parametersBiso mean: 50 Å2
Baniso -1Baniso -2Baniso -3
1--1.91 Å20 Å20 Å2
2--10.7 Å20 Å2
3----8.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.31 Å
Luzzati d res low-8 Å
Luzzati sigma a0.41 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9405 0 105 596 10106
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.352 230 4.7 %
Rwork0.287 4651 -
obs--97.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2FES_XPLOR_PAR.TXTION.TOP
X-RAY DIFFRACTION3COF.PARXDICT_1011.TOP
X-RAY DIFFRACTION4WATER.PARAM
X-RAY DIFFRACTION5ION.PARAM
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9

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