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- PDB-2w3s: Crystal Structure of Xanthine Dehydrogenase (desulfo form) from R... -

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Basic information

Entry
Database: PDB / ID: 2w3s
TitleCrystal Structure of Xanthine Dehydrogenase (desulfo form) from Rhodobacter capsulatus in Complex with Xanthine
Components(XANTHINE DEHYDROGENASE) x 2
KeywordsOXIDOREDUCTASE / XO / XDH / GOUT / IRON / XANTHINE / IRON-SULFUR / PURINE METABOLISM / MOLYBDENUM COFACTOR / HYPOXANTHINE / HYPERURICEMIA / METAL-BINDING
Function / homology
Function and homology information


1.1.1.204 / xanthine dehydrogenase activity / molybdenum ion binding / FAD binding / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / iron ion binding
Similarity search - Function
Xanthine dehydrogenase, small subunit, bacteria / Xanthine dehydrogenase, molybdopterin binding subunit / Xanthine dehydrogenase, small subunit / 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, bacteria / Xanthine dehydrogenase, molybdopterin binding subunit / Xanthine dehydrogenase, small subunit / 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. / Beta-grasp domain / FAD-binding, type PCMH, subdomain 2 / 2Fe-2S iron-sulfur cluster binding domain / 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 / HYDROXY(DIOXO)MOLYBDENUM / Chem-MTE / XANTHINE / Xanthine dehydrogenase / Xanthine dehydrogenase
Similarity search - Component
Biological speciesRHODOBACTER CAPSULATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsDietzel, U. / Kuper, J. / Leimkuhler, S. / Kisker, C.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Mechanism of Substrate and Inhibitor Binding of Rhodobacter Capsulatus Xanthine Dehydrogenase.
Authors: Dietzel, U. / Kuper, J. / Doebbler, J.A. / Schulte, A. / Truglio, J.J. / Leimkuhler, S. / Kisker, C.
History
DepositionNov 14, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _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_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_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_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 / _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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: XANTHINE DEHYDROGENASE
B: XANTHINE DEHYDROGENASE
C: XANTHINE DEHYDROGENASE
D: XANTHINE DEHYDROGENASE
E: XANTHINE DEHYDROGENASE
F: XANTHINE DEHYDROGENASE
G: XANTHINE DEHYDROGENASE
H: XANTHINE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)537,07336
Polymers529,5948
Non-polymers7,47928
Water68538
1
A: XANTHINE DEHYDROGENASE
B: XANTHINE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,2689
Polymers132,3992
Non-polymers1,8707
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7870 Å2
ΔGint-31.4 kcal/mol
Surface area49690 Å2
MethodPQS
2
C: XANTHINE DEHYDROGENASE
D: XANTHINE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,2689
Polymers132,3992
Non-polymers1,8707
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8030 Å2
ΔGint-32 kcal/mol
Surface area49470 Å2
MethodPQS
3
E: XANTHINE DEHYDROGENASE
F: XANTHINE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,2689
Polymers132,3992
Non-polymers1,8707
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8030 Å2
ΔGint-32.8 kcal/mol
Surface area49920 Å2
MethodPQS
4
G: XANTHINE DEHYDROGENASE
H: XANTHINE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,2689
Polymers132,3992
Non-polymers1,8707
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7930 Å2
ΔGint-31.6 kcal/mol
Surface area49490 Å2
MethodPQS
Unit cell
Length a, b, c (Å)92.830, 140.560, 158.170
Angle α, β, γ (deg.)109.60, 105.89, 101.18
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
12B
22D
32F
42H
13B
23D
33F
43H

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETPROPRO4AA1 - 4621 - 462
21METMETPROPRO4CC1 - 4621 - 462
31METMETPROPRO4EE1 - 4621 - 462
41METMETPROPRO4GG1 - 4621 - 462
12SERSERALAALA4BB2 - 7772 - 777
22SERSERALAALA4DD2 - 7772 - 777
32SERSERALAALA4FF2 - 7772 - 777
42SERSERALAALA4HH2 - 7772 - 777
13XANXANXANXAN1BN1780
23XANXANXANXAN1DU1780
33XANXANXANXAN1FBA1780
43XANXANXANXAN1HIA1780

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(-0.01118, -0.789, 0.6143), (-0.7952, -0.3654, -0.4838), (0.6062, -0.4939, -0.6233)0.2446, 0.1067, -0.1592
2given(-0.02362, -0.7888, 0.6142), (-0.7873, -0.3639, -0.4977), (0.6161, -0.4953, -0.6125)0.03229, 0.2031, 0.04947
3given(0.3308, -0.711, -0.6205), (0.8622, -0.03954, 0.505), (-0.3836, -0.7021, 0.5999)89.29, -24.53, 11.61
4given(-0.927, -0.375, -0.009707), (-0.3751, 0.927, 0.004463), (0.007325, 0.007777, -0.9999)23.79, -67.11, 60.16
5given(-0.9265, -0.3763, -0.006805), (-0.3763, 0.9265, 0.002571), (0.005337, 0.004943, -1)23.84, -66.98, 60.36
6given(0.3256, -0.7103, -0.624), (0.8696, -0.03414, 0.4926), (-0.3712, -0.703, 0.6066)89.55, -24.09, 10.88

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
XANTHINE DEHYDROGENASE /


Mass: 49420.508 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOBACTER CAPSULATUS (bacteria) / Plasmid: PSL207 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TP1000 / References: UniProt: O54050, 1.1.1.204
#2: Protein
XANTHINE DEHYDROGENASE /


Mass: 82978.031 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOBACTER CAPSULATUS (bacteria) / Plasmid: PSL207 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TP1000 / References: UniProt: O54051, 1.1.1.204

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Non-polymers , 7 types, 66 molecules

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


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


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: 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
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#7: Chemical
ChemComp-XAN / XANTHINE / Xanthine


Mass: 152.111 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H4N4O2
#8: Chemical
ChemComp-MOM / HYDROXY(DIOXO)MOLYBDENUM


Mass: 144.946 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: HMoO3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 3.36 Å3/Da / Density % sol: 59.8 % / Description: NONE
Crystal growpH: 8.3
Details: 100 MM TRIS PH 8.3, 8% PEG 8000,7.5MM BACL2, 25MM DTT, 3% ISOPROPANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 28, 2008
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.6→50.64 Å / Num. obs: 206556 / % possible obs: 97.8 % / Redundancy: 1.96 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.71
Reflection shellResolution: 2.6→2.62 Å / Redundancy: 1.94 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.08 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.5.0055refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JRO

1jro


Resolution: 2.6→50.12 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.859 / SU B: 12.775 / SU ML: 0.265 / Cross valid method: THROUGHOUT / ESU R: 0.537 / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.284 10343 5 %RANDOM
Rwork0.232 ---
obs0.234 196212 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å2-0.59 Å2-0.84 Å2
2---2.58 Å2-1.51 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms36372 0 404 38 36814
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02237644
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.97251136
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.34254824
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.83222.5931620
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.192155780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.33715368
X-RAY DIFFRACTIONr_chiral_restr0.090.25652
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02128980
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4491.524000
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.855238132
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.291313644
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1664.512988
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

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
31B22tight positional0.010.05
32D22tight positional00.05
33F22tight positional0.010.05
34H22tight positional0.010.05
11A3376medium positional0.340.5
12C3376medium positional0.30.5
13E3376medium positional0.350.5
14G3376medium positional0.350.5
21B5717medium positional0.260.5
22D5717medium positional0.250.5
23F5717medium positional0.270.5
24H5717medium positional0.290.5
31B22tight thermal0.030.5
32D22tight thermal0.020.5
33F22tight thermal0.020.5
34H22tight thermal0.040.5
11A3376medium thermal0.472
12C3376medium thermal1.052
13E3376medium thermal0.482
14G3376medium thermal0.552
21B5717medium thermal0.542
22D5717medium thermal0.762
23F5717medium thermal0.552
24H5717medium thermal0.692
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 742 -
Rwork0.337 14298 -
obs--96.23 %

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