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- PDB-1jrp: Crystal Structure of Xanthine Dehydrogenase inhibited by alloxant... -

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Basic information

Entry
Database: PDB / ID: 1jrp
TitleCrystal Structure of Xanthine Dehydrogenase inhibited by alloxanthine from Rhodobacter capsulatus
Components(xanthine dehydrogenase, chain ...) x 2
KeywordsOXIDOREDUCTASE / Partial Beta-Barrel / xdh / xo
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 / 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 / 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
Oxypurinol / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / DIOXOTHIOMOLYBDENUM(VI) ION / Chem-MTE / : / : / Xanthine dehydrogenase / Xanthine dehydrogenase
Similarity search - Component
Biological speciesRhodobacter capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsTruglio, J.J. / Theis, K. / Leimkuhler, S. / Rappa, R. / Rajagopalan, K.V. / Kisker, C.
CitationJournal: Structure / Year: 2002
Title: Crystal structures of the active and alloxanthine-inhibited forms of xanthine dehydrogenase from Rhodobacter capsulatus
Authors: Truglio, J.J. / Theis, K. / Leimkuhler, S. / Rappa, R. / Rajagopalan, K.V. / Kisker, C.
History
DepositionAug 14, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 10, 2014Group: Non-polymer description
Revision 1.4Apr 22, 2015Group: Non-polymer description
Revision 1.5Aug 16, 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_ref_seq_dif / 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_ref_seq_dif.details / _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, chain A
B: xanthine dehydrogenase, chain B
C: xanthine dehydrogenase, chain A
D: xanthine dehydrogenase, chain B
E: xanthine dehydrogenase, chain A
F: xanthine dehydrogenase, chain B
G: xanthine dehydrogenase, chain A
H: xanthine dehydrogenase, chain B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)536,84536
Polymers529,3028
Non-polymers7,54328
Water00
1
A: xanthine dehydrogenase, chain A
B: xanthine dehydrogenase, chain B
C: xanthine dehydrogenase, chain A
D: xanthine dehydrogenase, chain B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,42218
Polymers264,6514
Non-polymers3,77114
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24860 Å2
ΔGint-195 kcal/mol
Surface area76330 Å2
MethodPISA
2
E: xanthine dehydrogenase, chain A
F: xanthine dehydrogenase, chain B
G: xanthine dehydrogenase, chain A
H: xanthine dehydrogenase, chain B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,42218
Polymers264,6514
Non-polymers3,77114
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25000 Å2
ΔGint-191 kcal/mol
Surface area76330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.617, 140.728, 157.665
Angle α, β, γ (deg.)109.59, 105.84, 101.25
Int Tables number1
Cell settingtriclinic
Space group name H-MP1

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Components

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Xanthine dehydrogenase, chain ... , 2 types, 8 molecules ACEGBDFH

#1: Protein
xanthine dehydrogenase, chain A / E.C.1.1.1.204 / XD


Mass: 49347.453 Da / Num. of mol.: 4 / Fragment: chain A, residues 1-462
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Production host: Escherichia coli (E. coli) / References: EMBL: 2956674, UniProt: O54050*PLUS, 1.1.1.204
#2: Protein
xanthine dehydrogenase, chain B / E.C.1.1.1.204 / XD


Mass: 82978.031 Da / Num. of mol.: 4 / Fragment: chain B, residues 1-777
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Production host: Escherichia coli (E. coli) / References: EMBL: 13397863, UniProt: O54051*PLUS, 1.1.1.204

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Non-polymers , 6 types, 28 molecules

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


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


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


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#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-MOS / DIOXOTHIOMOLYBDENUM(VI) ION


Mass: 161.012 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: HMoO2S
#8: Chemical
ChemComp-141 / Oxypurinol / Alloxanthine


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

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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: 3.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG, Tris, DTT, isopropanol at pH 8.0, VAPOR DIFFUSION, HANGING DROP at 295K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
28 %PEG80001reservoir
37.5 mM1reservoirBaCl2
425 mMdithiothreitol1reservoir
53 %isopropanol1reservoir
60.1 MTris1reservoirpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 25, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. all: 135608 / Num. obs: 135608 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1000 / Redundancy: 4.1 % / Rsym value: 0.159 / Net I/σ(I): 10.1
Reflection shellResolution: 3→3.1 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.741
Reflection
*PLUS
Num. measured all: 551313 / Rmerge(I) obs: 0.159
Reflection shell
*PLUS
Rmerge(I) obs: 0.741

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
REFMAC5refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JRO

1jro


Resolution: 3→30 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.867 / SU B: 16.288 / SU ML: 0.31 / SU Rfree: 0.397 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -1000 / ESU R Free: 0.397
Details: FOUR-FOLD NCS RESTRAINTS WERE IMPOSED ON CHAINS A, B, C, D AND E, F, G, H
RfactorNum. reflection% reflectionSelection details
Rfree0.243 6818 5 %RANDOM
Rwork0.193 ---
all0.196 128790 --
obs0.196 128790 99.07 %-
Solvent computationSolvent model: BABINET MODEL WITH MAS
Displacement parametersBiso mean: 35.64 Å2
Baniso -1Baniso -2Baniso -3
1-1.7 Å2-0.37 Å20.01 Å2
2---2.65 Å2-1.92 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms36348 0 400 0 36748
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.02137354
X-RAY DIFFRACTIONr_angle_refined_deg2.7241.950829
X-RAY DIFFRACTIONr_chiral_restr0.1510.25655
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0228877
X-RAY DIFFRACTIONr_nbd_refined0.2190.53709
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.53709
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3950.320686
X-RAY DIFFRACTIONr_mcbond_it0.991.523984
X-RAY DIFFRACTIONr_mcangle_it1.871238100
X-RAY DIFFRACTIONr_scbond_it3.094313370
X-RAY DIFFRACTIONr_scangle_it5.0784.512709
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.375 491
Rwork0.255 9358
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.195 / Rfactor Rfree: 0.244
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.03
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.751
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it
LS refinement shell
*PLUS
Rfactor Rfree: 0.375 / Rfactor Rwork: 0.255

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