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- PDB-3ns1: Crystal Structure of Bovine Xanthine Oxidase in Complex with 6-Me... -

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Basic information

Entry
Database: PDB / ID: 3ns1
TitleCrystal Structure of Bovine Xanthine Oxidase in Complex with 6-Mercaptopurine
Components(Xanthine dehydrogenase/oxidase) x 3
KeywordsOXIDOREDUCTASE / xanthine oxidase / hypoxanthine / substrate orientation / hydroxylase
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 / 9H-purine-6-thiol / Xanthine dehydrogenase/oxidase
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCao, H. / Pauff, J.M. / Hille, R.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Substrate orientation and catalytic specificity in the action of xanthine oxidase: the sequential hydroxylation of hypoxanthine to uric acid.
Authors: Cao, H. / Pauff, J.M. / Hille, R.
History
DepositionJul 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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 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)273,67918
Polymers269,9876
Non-polymers3,69112
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30360 Å2
ΔGint-213 kcal/mol
Surface area83560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.636, 73.928, 140.353
Angle α, β, γ (deg.)90.000, 97.010, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21J
12B
22K
13C
23L

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRLYSLYSAA2 - 1651 - 164
21THRTHRLYSLYSJD2 - 1651 - 164
12PROPROGLYGLYBB224 - 5281 - 305
22PROPROGLYGLYKE224 - 5281 - 305
13ASPASPTHRTHRCC571 - 13151 - 745
23ASPASPTHRTHRLF571 - 13151 - 745

NCS ensembles :
ID
1
2
3

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Components

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Protein , 3 types, 6 molecules AJBKCL

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


Mass: 18002.881 Da / Num. of mol.: 2 / Fragment: iron-sulfur binding domain / Source method: isolated from a natural source / Details: milk / Source: (natural) Bos taurus (cattle)
References: UniProt: P80457, xanthine dehydrogenase, xanthine oxidase
#2: Protein Xanthine dehydrogenase/oxidase / Xanthine dehydrogenase / XD / Xanthine oxidase / XO / Xanthine oxidoreductase


Mass: 34024.590 Da / Num. of mol.: 2 / Fragment: flavin binding domain / Source method: isolated from a natural source / Details: milk / Source: (natural) Bos taurus (cattle)
References: UniProt: P80457, xanthine dehydrogenase, xanthine oxidase
#3: Protein Xanthine dehydrogenase/oxidase / Xanthine dehydrogenase / XD / Xanthine oxidase / XO / Xanthine oxidoreductase


Mass: 82966.203 Da / Num. of mol.: 2 / Fragment: molybdenum binding domain / Source method: isolated from a natural source / Details: milk / Source: (natural) Bos taurus (cattle)
References: UniProt: P80457, xanthine dehydrogenase, xanthine oxidase

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Non-polymers , 6 types, 299 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-PM6 / 9H-purine-6-thiol / 6-Mercaptopurine / Mercaptopurine


Mass: 152.177 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4N4S / Comment: medication*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.57 Å3/Da / Density % sol: 52.1 %
Crystal growTemperature: 298 K / Method: sitting batch / pH: 7 / Details: PEG 8000, pH 7.0, sitting batch, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.6→45.5 Å / Num. all: 84753 / Num. obs: 78350 / % possible obs: 92.4 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 27.1 Å2 / Net I/σ(I): 7.5
Reflection shellResolution: 2.6→2.668 Å / % possible all: 92.4

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
SCALAdata scaling
MOLREPCCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→45.5 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.875 / Occupancy max: 1 / Occupancy min: 1 / SU B: 11.285 / SU ML: 0.243 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.373 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2691 3922 5 %RANDOM
Rwork0.2169 ---
obs0.2195 78350 92.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.58 Å2 / Biso mean: 27.0715 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--1.72 Å20 Å2-0.19 Å2
2--0.25 Å20 Å2
3---1.42 Å2
Refinement stepCycle: LAST / Resolution: 2.6→45.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18872 0 198 287 19357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02219481
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.97426371
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.70852432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.49323.791815
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.837153337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.57815118
X-RAY DIFFRACTIONr_chiral_restr0.1120.22953
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214536
X-RAY DIFFRACTIONr_nbd_refined0.220.27350
X-RAY DIFFRACTIONr_nbtor_refined0.3060.213012
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2532
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3850.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.25
X-RAY DIFFRACTIONr_mcbond_it0.7111.512500
X-RAY DIFFRACTIONr_mcangle_it1.174219520
X-RAY DIFFRACTIONr_scbond_it1.82738070
X-RAY DIFFRACTIONr_scangle_it2.9364.56843
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1255TIGHT POSITIONAL0.060.05
1A1255TIGHT THERMAL0.150.5
2B2389TIGHT POSITIONAL0.070.05
2B2389TIGHT THERMAL0.130.5
3C5761TIGHT POSITIONAL0.070.05
3C5761TIGHT THERMAL0.150.5
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 285 -
Rwork0.312 5410 -
all-5695 -
obs--92.14 %

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