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- PDB-2w3r: Crystal Structure of Xanthine Dehydrogenase (desulfo form) from R... -

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Basic information

Entry
Database: PDB / ID: 2w3r
TitleCrystal Structure of Xanthine Dehydrogenase (desulfo form) from Rhodobacter capsulatus in complex with hypoxanthine
Components(XANTHINE DEHYDROGENASE) x 2
KeywordsOXIDOREDUCTASE / XDH / GOUT / IRON / XANTHINE / IRON-SULFUR / MOLYBDENUM COFACTOR / HYPOXANTHINE / 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 / HYPOXANTHINE / HYDROXY(DIOXO)MOLYBDENUM / Chem-MTE / Xanthine dehydrogenase / Xanthine dehydrogenase
Similarity search - Component
Biological speciesRHODOBACTER CAPSULATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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

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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)537,00936
Polymers529,5948
Non-polymers7,41528
Water1,45981
1
A: XANTHINE DEHYDROGENASE
B: XANTHINE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,2529
Polymers132,3992
Non-polymers1,8547
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10380 Å2
ΔGint-92.7 kcal/mol
Surface area40250 Å2
MethodPISA
2
C: XANTHINE DEHYDROGENASE
D: XANTHINE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,2529
Polymers132,3992
Non-polymers1,8547
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7170 Å2
ΔGint-53.7 kcal/mol
Surface area51090 Å2
MethodPISA
3
E: XANTHINE DEHYDROGENASE
F: XANTHINE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,2529
Polymers132,3992
Non-polymers1,8547
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10400 Å2
ΔGint-90.9 kcal/mol
Surface area40280 Å2
MethodPISA
4
G: XANTHINE DEHYDROGENASE
H: XANTHINE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,2529
Polymers132,3992
Non-polymers1,8547
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10330 Å2
ΔGint-91.2 kcal/mol
Surface area40300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.770, 139.940, 158.040
Angle α, β, γ (deg.)109.33, 106.15, 101.05
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
12B
22D
32F
42H

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETPROPROAA1 - 4621 - 462
21METMETPROPROCC1 - 4621 - 462
31METMETPROPROEE1 - 4621 - 462
41METMETPROPROGG1 - 4621 - 462
12SERSERALAALABB2 - 7772 - 777
22SERSERALAALADD2 - 7772 - 777
32SERSERALAALAFF2 - 7772 - 777
42SERSERALAALAHH2 - 7772 - 777

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.01833, -0.7885, 0.6147), (-0.7948, -0.3615, -0.4874), (0.6066, -0.4975, -0.6201)0.365, 0.1422, -0.2418
2given(-0.03257, -0.7879, 0.6149), (-0.7865, -0.3594, -0.5022), (0.6167, -0.5, -0.608)0.1498, 0.3116, 0.02197
3given(0.337, -0.7115, -0.6167), (0.8604, -0.03325, 0.5085), (-0.3823, -0.7019, 0.6009)89.06, -24.99, 11.49
4given(-0.9274, -0.3741, -0.008311), (-0.3741, 0.9274, 0.001513), (0.007141, 0.004512, -1)23.5, -66.76, 60.47
5given(-0.927, -0.375, -0.00655), (-0.375, 0.927, 0.000645), (0.00583, 0.003054, -1)23.64, -66.74, 60.55
6given(0.3305, -0.7132, -0.6182), (0.868, -0.02761, 0.4958), (-0.3707, -0.7005, 0.6099)89.41, -24.62, 10.55

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
XANTHINE DEHYDROGENASE / / XDHA


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 / / XDHB


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, 109 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-HPA / HYPOXANTHINE / Hypoxanthine


Mass: 136.111 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H4N4O
#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.: 81 / 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: 3.34 Å3/Da / Density % sol: 59.6 % / Description: NONE
Crystal growpH: 8.3
Details: 7.5 MM BACL2, 8% PEG 8000, 100 MM TRIS-HCL PH 8.3, 25 MM DTT AND 3% ISOPROPANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 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: 2.7→51.03 Å / Num. obs: 183839 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 1.97 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 6.4
Reflection shellResolution: 2.7→2.72 Å / Redundancy: 1.97 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 0.84 / % possible all: 97.7

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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: 2.9→51.23 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.852 / SU B: 19.624 / SU ML: 0.362 / Cross valid method: THROUGHOUT / ESU R Free: 0.426 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.281 7476 5 %RANDOM
Rwork0.24 ---
obs0.242 141476 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.09 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20.48 Å2-1.7 Å2
2---0.3 Å2-1.69 Å2
3----2.87 Å2
Refinement stepCycle: LAST / Resolution: 2.9→51.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms36372 0 400 81 36853
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02237592
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9831.9751060
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.83954824
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61622.5931620
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.407155780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.07715368
X-RAY DIFFRACTIONr_chiral_restr0.0620.25652
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02128932
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_it0.2191.524000
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.41238132
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.457313592
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.7724.512912
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
11A3376medium positional0.220.5
12C3376medium positional0.220.5
13E3376medium positional0.240.5
14G3376medium positional0.230.5
21B5717medium positional0.20.5
22D5717medium positional0.190.5
23F5717medium positional0.20.5
24H5717medium positional0.230.5
11A3376medium thermal0.122
12C3376medium thermal0.312
13E3376medium thermal0.172
14G3376medium thermal0.192
21B5717medium thermal0.162
22D5717medium thermal0.222
23F5717medium thermal0.172
24H5717medium thermal0.232
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 518 -
Rwork0.341 10328 -
obs--97.71 %

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