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- PDB-2ckj: Human milk xanthine oxidoreductase -

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Basic information

Entry
Database: PDB / ID: 2ckj
TitleHuman milk xanthine oxidoreductase
ComponentsXANTHINE OXIDOREDUCTASE
KeywordsOXIDOREDUCTASE / FAD / NAD / IRON / 2FE-2S / MOLYBDENUM / PEROXISOME / REVERSIBLE INTERCONVERSION / XANTHINE DEHYDROGENASE / XANTHINE OXIDOREDUCTASE / XANTHINE OXIDASE / IRON-SULFUR / POLYMORPHISM / FLAVOPROTEIN / METAL-BINDING
Function / homology
Function and homology information


hypoxanthine catabolic process / hypoxanthine dehydrogenase activity / hypoxanthine oxidase activity / negative regulation of vasculogenesis / guanine catabolic process / deoxyguanosine catabolic process / dGMP catabolic process / negative regulation of endothelial cell differentiation / xanthine dehydrogenase / xanthine oxidase ...hypoxanthine catabolic process / hypoxanthine dehydrogenase activity / hypoxanthine oxidase activity / negative regulation of vasculogenesis / guanine catabolic process / deoxyguanosine catabolic process / dGMP catabolic process / negative regulation of endothelial cell differentiation / xanthine dehydrogenase / xanthine oxidase / xanthine oxidase activity / xanthine catabolic process / xanthine dehydrogenase activity / GMP catabolic process / amide catabolic process / Butyrophilin (BTN) family interactions / deoxyinosine catabolic process / adenosine catabolic process / deoxyadenosine catabolic process / dAMP catabolic process / inosine catabolic process / negative regulation of vascular endothelial growth factor signaling pathway / AMP catabolic process / IMP catabolic process / Purine catabolism / allantoin metabolic process / molybdopterin cofactor binding / Azathioprine ADME / positive regulation of p38MAPK cascade / iron-sulfur cluster assembly / negative regulation of endothelial cell proliferation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / lactation / FAD binding / negative regulation of protein phosphorylation / sarcoplasmic reticulum / : / 2 iron, 2 sulfur cluster binding / positive regulation of reactive oxygen species metabolic process / peroxisome / flavin adenine dinucleotide binding / iron ion binding / negative regulation of gene expression / protein homodimerization activity / extracellular space / cytosol
Similarity search - Function
Xanthine dehydrogenase, small subunit / Oxidoreductase, molybdopterin binding site / Eukaryotic molybdopterin oxidoreductases signature. / CO dehydrogenase flavoprotein C-terminal 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 ...Xanthine dehydrogenase, small subunit / Oxidoreductase, molybdopterin binding site / Eukaryotic molybdopterin oxidoreductases signature. / CO dehydrogenase flavoprotein C-terminal 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 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 / FAD-binding, type PCMH, subdomain 1 / 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 / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / 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
Similarity search - Domain/homology
ACETIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / PHOSPHATE ION / Xanthine dehydrogenase/oxidase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.59 Å
AuthorsPearson, A.R. / Godber, B.L.J. / Eisenthal, R. / Taylor, G.L. / Harrison, R.
CitationJournal: To be Published
Title: Human Milk Xanthine Dehydrogenase is Incompletely Converted to the Oxidase Form in the Absence of Proteolysis. A Structural Explanation.
Authors: Pearson, A.R. / Godber, B.L.J. / Eisenthal, R. / Taylor, G.L. / Harrison, R.
History
DepositionApr 19, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: XANTHINE OXIDOREDUCTASE
B: XANTHINE OXIDOREDUCTASE
C: XANTHINE OXIDOREDUCTASE
D: XANTHINE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)591,47922
Polymers586,4074
Non-polymers5,07218
Water00
1
A: XANTHINE OXIDOREDUCTASE
hetero molecules

A: XANTHINE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,66210
Polymers293,2042
Non-polymers2,4598
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
MethodPQS
2
B: XANTHINE OXIDOREDUCTASE
hetero molecules

B: XANTHINE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,66210
Polymers293,2042
Non-polymers2,4598
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
MethodPQS
3
C: XANTHINE OXIDOREDUCTASE
D: XANTHINE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,81712
Polymers293,2042
Non-polymers2,61410
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)197.734, 197.734, 285.538
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A6 - 422
2111B6 - 422
3111C6 - 422
4111D6 - 422
1211A435 - 503
2211B435 - 503
3211C435 - 503
4211D435 - 503
1311A515 - 523
2311B515 - 523
3311C515 - 523
4311D515 - 523
1411A557 - 590
2411B557 - 590
3411C557 - 590
4411D557 - 590
1511A600 - 745
2511B600 - 745
3511C600 - 745
4511D600 - 745
1611A755 - 1310
2611B755 - 1310
3611C755 - 1310
4611D755 - 1310
1711A3001 - 3006
2711B3001 - 3006
3711C3001 - 3006
4711D3001 - 3006

NCS oper:
IDCodeMatrixVector
1given(-0.507, -0.862, -0.006), (-0.862, 0.507, -0.023), (0.023, -0.007, -1)97.69203, 173.79907, 237.25742
2given(0.462, -0.886, 0.029), (0.887, 0.463, 0.009), (-0.021, 0.022, 1)39.08794, -63.1065, -25.20313
3given(-0.999, -0.033, -0.032), (-0.033, 0.999, -0.002), (0.032, -0.001, -0.999)46.84574, -62.02838, 259.46573

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
XANTHINE OXIDOREDUCTASE / XDH / XANTHINE DEHYDROGENASE / XO / XANTHINE OXIDASE / OXIDOREDUCTASE


Mass: 146601.781 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: MILK KINDLY DONATED BY MOTHERS AT THE INTENSIVE CARE BABY UNITS AT THE BRISTOL ROYAL INFIRMARY AND SOUTHMEAD HOSPITAL, BRISTOL, UK
Source: (natural) HOMO SAPIENS (human) / Tissue: BREAST MILK
References: UniProt: P47989, 1.1.1.204, EC: 1.2.3.2, xanthine oxidase

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Non-polymers , 5 types, 18 molecules

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


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


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4

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Details

Has protein modificationY

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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: 2.7 Å3/Da / Density % sol: 53.8 %
Crystal growpH: 6
Details: 26% (W/V) PEG 4K, 0.1M SODIUM ACETATE, PH 6, 0.25M AMMONIUM ACETATE, 10MM DTT, 10% (W/V) GLUCOSE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9326
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9326 Å / Relative weight: 1
ReflectionResolution: 3.5→30 Å / Num. obs: 75088 / % possible obs: 98.2 % / Observed criterion σ(I): 1.5 / Redundancy: 4.4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 3.6
Reflection shellResolution: 3.5→3.62 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.5 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FO4

1fo4


Resolution: 3.59→30.76 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.841 / SU B: 68.993 / SU ML: 0.511 / Cross valid method: THROUGHOUT / ESU R Free: 0.71 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES A1-2, A166-192, A426-429, A534-557, A1231-A1328, A1330-1333, B1, B166-192, B548-556, B1320-1325, B1333, C1-2, C166-192, C429-431, ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES A1-2, A166-192, A426-429, A534-557, A1231-A1328, A1330-1333, B1, B166-192, B548-556, B1320-1325, B1333, C1-2, C166-192, C429-431, C548-556, C1320-1327, C1333, D1-2, D166-192, D542-556, D1321-1325, D1333 ARE NOT PRESENT IN THE ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.258 3745 5 %RANDOM
Rwork0.178 ---
obs0.182 70696 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.75 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.59→30.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39530 0 277 0 39807
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0450.02240686
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.4611.97255080
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg15.0855101
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.73823.9681681
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.79156980
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.10615242
X-RAY DIFFRACTIONr_chiral_restr0.2210.26192
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0230316
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3170.216918
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3540.226141
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2180.21154
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.360.2110
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1931.527044
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.759241134
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.564316864
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9934.513890
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 9345 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.140.05
2Btight positional0.140.05
3Ctight positional0.140.05
4Dtight positional0.150.05
1Atight thermal0.250.5
2Btight thermal0.250.5
3Ctight thermal0.260.5
4Dtight thermal0.260.5
LS refinement shellResolution: 3.59→3.68 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.277 244
Rwork0.181 4917
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.51550.2349-0.1480.68170.10510.38-0.0058-0.1876-0.2273-0.12160.0291-0.19610.09420.1721-0.0233-0.44470.0333-0.029-0.45120.0442-0.505388.78789.394137.152
20.8937-0.1702-0.01510.8879-0.08630.31090.0176-0.0546-0.3802-0.0422-0.0254-0.00330.08050.00320.0079-0.50140.0032-0.0484-0.58420.0071-0.462-25.145139.338101.533
30.6626-0.28580.03670.7838-0.09930.4619-0.0539-0.04120.1360.15640.0506-0.35960.02510.12510.0033-0.47510.0464-0.1349-0.5883-0.0738-0.44274.96858.133112.002
40.2503-0.0031-0.07850.8149-0.16830.5802-0.01410.01-0.0078-0.06880.06190.18780.2281-0.1993-0.0478-0.275-0.0743-0.1325-0.52640.0381-0.5614-49.18924.034125.044
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 1318
2X-RAY DIFFRACTION2B2 - 1318
3X-RAY DIFFRACTION3C2 - 1318
4X-RAY DIFFRACTION4D2 - 1318

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