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- PDB-3eub: Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine -

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Basic information

Entry
Database: PDB / ID: 3eub
TitleCrystal Structure of Desulfo-Xanthine Oxidase with Xanthine
Components(Xanthine dehydrogenase/oxidase) x 3
KeywordsOXIDOREDUCTASE / enzyme catalysis / desulfo / substrate orientation / xanthine / 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 / [2Fe-2S]-binding domain / CO dehydrogenase flavoprotein C-terminal domain / Aldehyde Oxidoreductase; domain 4 / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain / Molybdopterin dehydrogenase, FAD-binding / CO dehydrogenase flavoprotein, C-terminal ...Xanthine dehydrogenase, small subunit / Oxidoreductase, molybdopterin binding site / Eukaryotic molybdopterin oxidoreductases signature. / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / [2Fe-2S]-binding domain / CO dehydrogenase flavoprotein C-terminal domain / Aldehyde Oxidoreductase; domain 4 / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin 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 / 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 / Aldehyde Oxidoreductase; domain 3 / FAD-binding, type PCMH, subdomain 1 / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / 2Fe-2S iron-sulfur cluster binding domain / 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 / DNA polymerase; domain 1 / Ubiquitin-like (UB roll) / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / HYDROXY(DIOXO)MOLYBDENUM / Chem-MTE / XANTHINE / Xanthine dehydrogenase/oxidase
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 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 9, 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 17, 2014Group: Database references
Revision 1.3Sep 6, 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 dehydrogenase/oxidase
B: Xanthine dehydrogenase/oxidase
C: Xanthine dehydrogenase/oxidase
J: Xanthine dehydrogenase/oxidase
K: Xanthine dehydrogenase/oxidase
L: Xanthine dehydrogenase/oxidase
S: Xanthine dehydrogenase/oxidase
T: Xanthine dehydrogenase/oxidase
U: Xanthine dehydrogenase/oxidase
2: Xanthine dehydrogenase/oxidase
3: Xanthine dehydrogenase/oxidase
4: Xanthine dehydrogenase/oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)551,29436
Polymers543,97612
Non-polymers7,31824
Water00
1
A: Xanthine dehydrogenase/oxidase
B: Xanthine dehydrogenase/oxidase
C: Xanthine dehydrogenase/oxidase
J: Xanthine dehydrogenase/oxidase
K: Xanthine dehydrogenase/oxidase
L: Xanthine dehydrogenase/oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)275,64718
Polymers271,9886
Non-polymers3,65912
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31470 Å2
ΔGint-189 kcal/mol
Surface area79860 Å2
MethodPISA
2
S: Xanthine dehydrogenase/oxidase
T: Xanthine dehydrogenase/oxidase
U: Xanthine dehydrogenase/oxidase
2: Xanthine dehydrogenase/oxidase
3: Xanthine dehydrogenase/oxidase
4: Xanthine dehydrogenase/oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)275,64718
Polymers271,9886
Non-polymers3,65912
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31800 Å2
ΔGint-194 kcal/mol
Surface area80420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.298, 133.176, 142.633
Angle α, β, γ (deg.)96.88, 93.11, 90.02
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A D
12B E
13C F
14G J
15H K
16I L

NCS domain segments:

Dom-ID: 1 / Refine code: 1

Component-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA4 - 1654 - 165
21DD4 - 1654 - 165
12BB224 - 527224 - 527
22EE226 - 527226 - 527
13CC571 - 1315571 - 1315
23FF571 - 1315571 - 1315
14GG3 - 1633 - 163
24JJ2 - 1652 - 165
15HH224 - 528224 - 528
25KK224 - 528224 - 528
16II571 - 1315571 - 1315
26LL571 - 1326571 - 1326

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 3 types, 12 molecules AJS2BKT3CLU4

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


Mass: 18134.078 Da / Num. of mol.: 4 / Fragment: 2Fe-2S ferredoxin-type domain, residues 1-165 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Secretion: Bovine Milk
References: UniProt: P80457, xanthine dehydrogenase, xanthine oxidase
#2: Protein
Xanthine dehydrogenase/oxidase / XD / XO / Xanthine oxidoreductase


Mass: 34024.590 Da / Num. of mol.: 4 / Fragment: AD-binding PCMH-type domain, residues 224-528 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Secretion: Bovine Milk
References: UniProt: P80457, xanthine dehydrogenase, xanthine oxidase
#3: Protein
Xanthine dehydrogenase/oxidase / XD / XO / Xanthine oxidoreductase


Mass: 83835.273 Da / Num. of mol.: 4 / Fragment: residues 571-1332 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Secretion: Bovine Milk
References: UniProt: P80457, xanthine dehydrogenase, xanthine oxidase

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Non-polymers , 5 types, 24 molecules

#4: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe2S2
#5: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: C10H14N5O6PS2
#7: Chemical
ChemComp-MOM / HYDROXY(DIOXO)MOLYBDENUM


Mass: 144.946 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: HMoO3
#8: Chemical
ChemComp-XAN / XANTHINE


Mass: 152.111 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H4N4O2

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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: 2.54 Å3/Da / Density % sol: 51.52 %
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: MAR CCD 165 mm / Detector: CCD / Date: Mar 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.6→141.42 Å / Num. obs: 119504
Reflection shellResolution: 2.6→2.668 Å / Num. unique all: 5403

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.72 Å33.17 Å
Translation2.72 Å33.17 Å

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FIQ

1fiq


Resolution: 2.6→33.08 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.826 / WRfactor Rfree: 0.308 / WRfactor Rwork: 0.246 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.823 / SU B: 12.029 / SU ML: 0.263 / SU Rfree: 0.457 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.457 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, MOM IS IN THE DESULFO FORM WITH AN ADDITIONAL OXYGEN IN PLACE OF THE SULFUR IN THE COORDINATION SPHERE
RfactorNum. reflection% reflectionSelection details
Rfree0.268 6008 5 %RANDOM
Rwork0.214 ---
obs0.217 119504 72.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 50.14 Å2 / Biso mean: 13.895 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å2-0.07 Å20.03 Å2
2---1.89 Å20.68 Å2
3---2.5 Å2
Refinement stepCycle: LAST / Resolution: 2.6→33.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37670 0 400 0 38070
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02238891
X-RAY DIFFRACTIONr_angle_refined_deg1.6591.97452648
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.80654852
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.8423.7881629
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.897156665
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.03415236
X-RAY DIFFRACTIONr_chiral_restr0.1070.25893
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0229024
X-RAY DIFFRACTIONr_nbd_refined0.2350.217851
X-RAY DIFFRACTIONr_nbtor_refined0.3140.226471
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.21320
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3850.2120
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2860.24
X-RAY DIFFRACTIONr_mcbond_it0.6151.524764
X-RAY DIFFRACTIONr_mcangle_it1.034238948
X-RAY DIFFRACTIONr_scbond_it1.553316119
X-RAY DIFFRACTIONr_scangle_it2.5444.513684
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1243TIGHT POSITIONAL0.070.05
1A1243TIGHT THERMAL0.140.5
2B2369TIGHT POSITIONAL0.070.05
2B2369TIGHT THERMAL0.120.5
3C5753TIGHT POSITIONAL0.070.05
3C5753TIGHT THERMAL0.130.5
4S1234TIGHT POSITIONAL0.070.05
4S1234TIGHT THERMAL0.140.5
5T2389TIGHT POSITIONAL0.060.05
5T2389TIGHT THERMAL0.110.5
6U5761TIGHT POSITIONAL0.070.05
6U5761TIGHT THERMAL0.130.5
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 300 -
Rwork0.265 5403 -
all-5703 -
obs--46.82 %

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