1FIQ

CRYSTAL STRUCTURE OF XANTHINE OXIDASE FROM BOVINE MILK

> Summary

Summary for 1FIQ

Related1FO4
DescriptorXANTHINE OXIDASE (E.C.1.1.3.22)
Functional Keywordsxanthine oxidase, oxidoreductase
Biological sourceBos taurus (cattle)
Cellular locationCytoplasm (By similarity) P80457 P80457 P80457
Total number of polymer chains3
Total molecular weight148954.25
Authors
Enroth, C.,Eger, B.T.,Okamoto, K.,Nishino, T.,Nishino, T.,Pai, E.F. (deposition date: 2000-08-04, release date: 2000-10-04, modification date: 2011-07-13)
Primary citation
Enroth, C.,Eger, B.T.,Okamoto, K.,Nishino, T.,Nishino, T.,Pai, E.F.
Crystal structures of bovine milk xanthine dehydrogenase and xanthine oxidase: structure-based mechanism of conversion.
Proc.Natl.Acad.Sci.USA, 97:10723-10728, 2000
PubMed: 11005854
DOI: 10.1073/pnas.97.20.10723
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.5 Å)
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Structure validation

ClashscoreRamachandran outliersSidechain outliers191.5%1.8%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 1fiq
no rotation
Molmil generated image of 1fiq
rotated about x axis by 90°
Molmil generated image of 1fiq
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 1fiq
no rotation
Molmil generated image of 1fiq
rotated about x axis by 90°
Molmil generated image of 1fiq
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (1fiq.pdb1.gz [409.4 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
AXANTHINE OXIDASEpolymer21924036.91
UniProt (P80457)
Pfam (PF00111)
Pfam (PF01799)
Bos taurus (cattle)@PDBjXO
BXANTHINE OXIDASEpolymer35039028.61
UniProt (P80457)
Pfam (PF00941)
Pfam (PF03450)
Bos taurus (cattle)@PDBjXO
CXANTHINE OXIDASEpolymer76383965.01
UniProt (P80457)
Pfam (PF01315)
Pfam (PF02738)
Bos taurus (cattle)@PDBjXO
FE2/S2 (INORGANIC) CLUSTERnon-polymer175.82
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)ESTERnon-polymer395.31
DIOXOTHIOMOLYBDENUM(VI) IONnon-polymer161.01
2-HYDROXYBENZOIC ACIDnon-polymer138.11
FLAVIN-ADENINE DINUCLEOTIDEnon-polymer785.61
GLYCEROLnon-polymer92.11
waterwater18.0596

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains3
Total molecular weight147030.5
Non-Polymers*Number of molecules7
Total molecular weight1923.8
All*Total molecular weight148954.2
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.5 Å)
Cell axes117.831165.403154.447
Cell angles90.0090.0090.00
SpacegroupC 2 2 21
Resolution limits8.00 - 2.50
the highest resolution shell value2.590 - 2.500
R-factor0.212
R-work0.21200
the highest resolution shell value0.287
R-free0.27500
the highest resolution shell value0.352
RMSD bond length0.013
RMSD bond angle1.400 (23.300*)

Data Collection Statistics

Resolution limits30.00 - 2.50
the highest resolution shell value -
Number of reflections51300*
Completeness97.9
the highest resolution shell value97.5*
I/sigma(I)-3

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1unknown*K*

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0005829cellular_componentcytosol
A0005615cellular_componentextracellular space
A0005777cellular_componentperoxisome
A0051537molecular_function2 iron, 2 sulfur cluster binding
A0009055molecular_functionelectron carrier activity
A0050660molecular_functionflavin adenine dinucleotide binding
A0005506molecular_functioniron ion binding
A0043546molecular_functionmolybdopterin cofactor binding
A0016614molecular_functionoxidoreductase activity, acting on CH-OH group of donors
A0016903molecular_functionoxidoreductase activity, acting on the aldehyde or oxo group of donors
A0004854molecular_functionxanthine dehydrogenase activity
A0004855molecular_functionxanthine oxidase activity
A0009115biological_processxanthine catabolic process
B0005829cellular_componentcytosol
B0005615cellular_componentextracellular space
B0005777cellular_componentperoxisome
B0051537molecular_function2 iron, 2 sulfur cluster binding
B0009055molecular_functionelectron carrier activity
B0050660molecular_functionflavin adenine dinucleotide binding
B0005506molecular_functioniron ion binding
B0043546molecular_functionmolybdopterin cofactor binding
B0016614molecular_functionoxidoreductase activity, acting on CH-OH group of donors
B0016903molecular_functionoxidoreductase activity, acting on the aldehyde or oxo group of donors
B0004854molecular_functionxanthine dehydrogenase activity
B0004855molecular_functionxanthine oxidase activity
B0009115biological_processxanthine catabolic process
C0005829cellular_componentcytosol
C0005615cellular_componentextracellular space
C0005777cellular_componentperoxisome
C0051537molecular_function2 iron, 2 sulfur cluster binding
C0009055molecular_functionelectron carrier activity
C0050660molecular_functionflavin adenine dinucleotide binding
C0005506molecular_functioniron ion binding
C0043546molecular_functionmolybdopterin cofactor binding
C0016614molecular_functionoxidoreductase activity, acting on CH-OH group of donors
C0016903molecular_functionoxidoreductase activity, acting on the aldehyde or oxo group of donors
C0004854molecular_functionxanthine dehydrogenase activity
C0004855molecular_functionxanthine oxidase activity
C0009115biological_processxanthine catabolic process
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC17BINDING SITE FOR RESIDUE FES A 601
ChainResidue
AGLN112
ACYS113
AGLY114
ACYS116
ACYS148
AARG149
ACYS150

AC210BINDING SITE FOR RESIDUE FES A 602
ChainResidue
AGLY42
ACYS43
AGLY44
AGLY46
AGLY47
ACYS48
AGLY49
ACYS51
AASN71
ACYS73

AC320BINDING SITE FOR RESIDUE MTE C 1333
ChainResidue
AGLN112
ACYS150
CGLY227
CGLY228
CPHE229
CARG343
CMET469
CGLY470
CGLN471
CALA509
CALA510
CSER511
CVAL512
CSER513
CGLN625
CGLU692
CMOS
CHOH
CHOH
CHOH

AC410BINDING SITE FOR RESIDUE MOS C 1334
ChainResidue
CGLN198
CPHE229
CGLY230
CPHE342
CARG343
CALA509
CALA510
CGLU692
CMTE
CSAL

AC59BINDING SITE FOR RESIDUE SAL C 1335
ChainResidue
CGLU233
CARG311
CPHE345
CSER439
CPHE440
CTHR441
CVAL442
CMOS
CHOH

AC624BINDING SITE FOR RESIDUE FAD B 606
ChainResidue
AGLU45
AGLY46
BLYS37
BLEU38
BVAL39
BVAL40
BGLY41
BASN42
BTHR43
BGLU44
BILE45
BLEU68
BPHE118
BALA119
BALA127
BSER128
BGLY131
BASN132
BILE134
BTHR135
BSER140
BASP141
BLEU185
BHOH

AC79BINDING SITE FOR RESIDUE GOL C 1336
ChainResidue
CARG270
CHIS271
CILE308
CTHR340
CALA341
CPHE342
CPHE345
CGLY346
CGLN349

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
FES_1fiq_A_60214FE2/S2 (INORGANIC) CLUSTER binding site
ChainResidueligand
ALYS40-CYS51FES: FE2/S2 (INORGANIC) CLUSTER
AASN71FES: FE2/S2 (INORGANIC) CLUSTER
ACYS73FES: FE2/S2 (INORGANIC) CLUSTER

FAD_1fiq_B_60640FLAVIN-ADENINE DINUCLEOTIDE binding site
ChainResidueligand
AGLU45-GLY47FAD: FLAVIN-ADENINE DINUCLEOTIDE
ALEU74FAD: FLAVIN-ADENINE DINUCLEOTIDE
BLYS256-GLY265FAD: FLAVIN-ADENINE DINUCLEOTIDE
BGLU267FAD: FLAVIN-ADENINE DINUCLEOTIDE
BLEU287FAD: FLAVIN-ADENINE DINUCLEOTIDE
BALA301FAD: FLAVIN-ADENINE DINUCLEOTIDE
BLEU305FAD: FLAVIN-ADENINE DINUCLEOTIDE
BTRP336-ALA338FAD: FLAVIN-ADENINE DINUCLEOTIDE
BVAL342FAD: FLAVIN-ADENINE DINUCLEOTIDE
BVAL345-SER347FAD: FLAVIN-ADENINE DINUCLEOTIDE
BGLY349-ASN351FAD: FLAVIN-ADENINE DINUCLEOTIDE
BILE353-THR354FAD: FLAVIN-ADENINE DINUCLEOTIDE
BILE358-LEU361FAD: FLAVIN-ADENINE DINUCLEOTIDE
BLEU398FAD: FLAVIN-ADENINE DINUCLEOTIDE
BGLU402-LEU404FAD: FLAVIN-ADENINE DINUCLEOTIDE
BLYS422FAD: FLAVIN-ADENINE DINUCLEOTIDE
BLYS433FAD: FLAVIN-ADENINE DINUCLEOTIDE

FES_1fiq_A_60114FE2/S2 (INORGANIC) CLUSTER binding site
ChainResidueligand
AGLY110-THR117FES: FE2/S2 (INORGANIC) CLUSTER
ALEU147-THR151FES: FE2/S2 (INORGANIC) CLUSTER
CLEU744FES: FE2/S2 (INORGANIC) CLUSTER

MTE_1fiq_C_133323PHOSPHONIC 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 binding site
ChainResidueligand
AGLN112-CYS113MTE: 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
ACYS150MTE: 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
CGLY796-GLY799MTE: 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
CPHE911-ARG912MTE: 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
CMET1038-GLN1040MTE: 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
CLEU1042MTE: 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
CTHR1077-THR1083MTE: 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
CGLN1194MTE: 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
CGLY1260-GLU1261MTE: 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

MOS_1fiq_C_133413DIOXOTHIOMOLYBDENUM(VI) ION binding site
ChainResidueligand
CGLN767MOS: DIOXOTHIOMOLYBDENUM(VI) ION
CPHE798-GLY799MOS: DIOXOTHIOMOLYBDENUM(VI) ION
CGLU802MOS: DIOXOTHIOMOLYBDENUM(VI) ION
CALA910-PHE914MOS: DIOXOTHIOMOLYBDENUM(VI) ION
CTHR1077-ALA1079MOS: DIOXOTHIOMOLYBDENUM(VI) ION
CGLU1261MOS: DIOXOTHIOMOLYBDENUM(VI) ION

SAL_1fiq_C_1335122-HYDROXYBENZOIC ACID binding site
ChainResidueligand
CGLU802SAL: 2-HYDROXYBENZOIC ACID
CLEU873SAL: 2-HYDROXYBENZOIC ACID
CSER876SAL: 2-HYDROXYBENZOIC ACID
CARG880SAL: 2-HYDROXYBENZOIC ACID
CPHE914SAL: 2-HYDROXYBENZOIC ACID
CSER1008-VAL1011SAL: 2-HYDROXYBENZOIC ACID
CLEU1014SAL: 2-HYDROXYBENZOIC ACID
CALA1078-ALA1079SAL: 2-HYDROXYBENZOIC ACID

GOL_1fiq_C_133613GLYCEROL binding site
ChainResidueligand
CGLY838-HIS840GOL: GLYCEROL
CILE877GOL: GLYCEROL
CTHR909-PHE911GOL: GLYCEROL
CGLY913-GLN918GOL: GLYCEROL

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
PS005591Eukaryotic molybdopterin oxidoreductases signature. [GA]-{A}-x(2)-[KRNQHT]-x(11,14)-[LIVMFYWS]-x(3)-{V}-{GK}-x(3)-[LIVMF]-x
ChainResidueDetails
CNA*

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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
SWS_FT_FI11Proton acceptor.
ChainResidueDetails
ANA*

SWS_FT_FI73Substrate.
ChainResidueDetails
ANA*
ANA*
ANA*

SWS_FT_FI83FAD.
ChainResidueDetails
ANA*
ANA*
ANA*

SWS_FT_FI91FAD; via amide nitrogen and carbonyl oxygen.
ChainResidueDetails
ANA*

SWS_FT_FI101Substrate; via amide nitrogen.
ChainResidueDetails
ANA*

SWS_FT_FI112FAD.
ChainResidueDetails
ANA*
ANA*

SWS_FT_FI121Proton acceptor.
ChainResidueDetails
BNA*

SWS_FT_FI183Substrate.
ChainResidueDetails
BNA*
BNA*
BNA*

SWS_FT_FI193FAD.
ChainResidueDetails
BPHE118
BASP141
BLYS203

SWS_FT_FI201FAD; via amide nitrogen and carbonyl oxygen.
ChainResidueDetails
BLEU185

SWS_FT_FI211Substrate; via amide nitrogen.
ChainResidueDetails
BNA*

SWS_FT_FI222FAD.
ChainResidueDetails
BNA*
BNA*

SWS_FT_FI231Proton acceptor.
ChainResidueDetails
CGLU692

SWS_FT_FI293Substrate.
ChainResidueDetails
CGLU233
CARG311
CPHE345

SWS_FT_FI303FAD.
ChainResidueDetails
CNA*
CNA*
CNA*

SWS_FT_FI311FAD; via amide nitrogen and carbonyl oxygen.
ChainResidueDetails
CNA*

SWS_FT_FI321Substrate; via amide nitrogen.
ChainResidueDetails
CTHR441

SWS_FT_FI332FAD.
ChainResidueDetails
CNA*
CNA*

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Catalytic Information from CSA

site_idNumber of ResiduesDetails
CSA13a catalytic site defined by CSA, PubMed 19109252, 15148401
ChainResidueDetails
CGLU1261
CARG880
CGLU802

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Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

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