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- PDB-1jro: Crystal Structure of Xanthine Dehydrogenase from Rhodobacter caps... -

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Basic information

Entry
Database: PDB / ID: 1jro
TitleCrystal Structure of Xanthine Dehydrogenase 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
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: 2.7 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 1.3Apr 22, 2015Group: Non-polymer description
Revision 1.4Aug 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)536,23632
Polymers529,3028
Non-polymers6,93524
Water2,216123
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)268,11816
Polymers264,6514
Non-polymers3,46712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24380 Å2
ΔGint-197 kcal/mol
Surface area76990 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)268,11816
Polymers264,6514
Non-polymers3,46712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24420 Å2
ΔGint-201 kcal/mol
Surface area76840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.875, 141.053, 158.113
Angle α, β, γ (deg.)109.53, 105.83, 101.33
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, 147 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2

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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

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X26C11.1
SYNCHROTRONNSLS X2521.1
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDFeb 14, 2001
CUSTOM-MADE2CCDMar 12, 2001
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 187987 / Num. obs: 187987 / % possible obs: 99.2 % / Observed criterion σ(I): -1000 / Redundancy: 3.8 % / Rsym value: 0.17 / Net I/σ(I): 11.2
Reflection shellResolution: 2.7→2.8 Å / % possible obs: 98 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.73
Reflection
*PLUS
Num. measured all: 722868 / Rmerge(I) obs: 0.161
Reflection shell
*PLUS
Rmerge(I) obs: 0.73

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FO4

1fo4


Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.887 / SU B: 11.3 / SU ML: 0.2 / SU Rfree: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.6
Details: FOUR-FOLD NCS RESTRAINTS WERE IMPOSED ON CHAINS A, B, C, D AND E, F, G, H
RfactorNum. reflection% reflectionSelection details
Rfree0.25154 9424 5 %RANDOM
Rwork0.21311 ---
all0.215 178563 --
obs0.21505 178563 99.18 %-
Solvent computationSolvent model: BABINET MODEL WITH MAS
Displacement parametersBiso mean: 39.67 Å2
Baniso -1Baniso -2Baniso -3
1-1.31 Å20.3 Å20.37 Å2
2---1.57 Å2-0.91 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms36348 0 360 123 36831
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.02137259
X-RAY DIFFRACTIONr_angle_refined_deg2.3461.950687
X-RAY DIFFRACTIONr_chiral_restr0.1420.25652
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0228808
X-RAY DIFFRACTIONr_nbd_refined0.1770.53190
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.53190
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2910.317820
X-RAY DIFFRACTIONr_mcbond_it1.0681.523984
X-RAY DIFFRACTIONr_mcangle_it2.03238100
X-RAY DIFFRACTIONr_scbond_it3.409313275
X-RAY DIFFRACTIONr_scangle_it5.5764.512571
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.377 688
Rwork0.286 13129
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 39.67 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.025
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.365
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: 0.377 / Rfactor Rwork: 0.286

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