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- PDB-7dqx: Crystal structure of xanthine dehydrogenase family protein -

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Basic information

Entry
Database: PDB / ID: 7dqx
TitleCrystal structure of xanthine dehydrogenase family protein
Components(6-hydroxypseudooxynicotine dehydrogenase complex subunit ...) x 4
KeywordsOXIDOREDUCTASE / KDH
Function / homology
Function and homology information


6-hydroxypseudooxynicotine dehydrogenase / 6-hydroxypseudooxynicotine dehydrogenase activity / nicotine catabolic process / FAD binding / 2 iron, 2 sulfur cluster binding / metal ion binding
Similarity search - Function
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 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 ...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 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 / 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. / FAD-binding, type PCMH, subdomain 2 / 2Fe-2S iron-sulfur cluster binding domain / 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
FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / PTERIN CYTOSINE DINUCLEOTIDE / MOLYBDENUM ATOM / 6-hydroxypseudooxynicotine dehydrogenase complex subunit alpha / 6-hydroxypseudooxynicotine dehydrogenase complex subunit beta / 6-hydroxypseudooxynicotine dehydrogenase complex subunit gamma
Similarity search - Component
Biological speciesPaenarthrobacter nicotinovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.44 Å
AuthorsLei, W.
CitationJournal: To Be Published
Title: crystal structure of xanthine dehydrogenase family protein
Authors: Lei, W.
History
DepositionDec 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6-hydroxypseudooxynicotine dehydrogenase complex subunit gamma
B: 6-hydroxypseudooxynicotine dehydrogenase complex subunit alpha
C: 6-hydroxypseudooxynicotine dehydrogenase complex subunit beta
E: 6-hydroxypseudooxynicotine dehydrogenase complex subunit alpha
F: 6-hydroxypseudooxynicotine dehydrogenase complex subunit beta
D: 6-hydroxypseudooxynicotine dehydrogenase complex subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)275,07016
Polymers271,2116
Non-polymers3,85910
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29230 Å2
ΔGint-190 kcal/mol
Surface area83960 Å2
Unit cell
Length a, b, c (Å)112.860, 126.792, 294.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E
13C
23F

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNASNASNASNAA21 - 79021 - 790
221ASNASNASNASNDF21 - 79021 - 790
132METMETARGARGBB1 - 2861 - 286
242METMETARGARGED1 - 2861 - 286
153METMETASPASPCC1 - 1601 - 160
263METMETASPASPFE1 - 1601 - 160

NCS ensembles :
ID
1
2
3

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Components

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6-hydroxypseudooxynicotine dehydrogenase complex subunit ... , 4 types, 6 molecules ADBCFE

#1: Protein 6-hydroxypseudooxynicotine dehydrogenase complex subunit gamma / / molybdopterin-binding subunit L / Ketone dehydrogenase large molybdopterin subunit


Mass: 86474.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenarthrobacter nicotinovorans (bacteria)
Gene: kdhC, kdhL / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q933N0, 6-hydroxypseudooxynicotine dehydrogenase
#2: Protein 6-hydroxypseudooxynicotine dehydrogenase complex subunit alpha / / molybdopterin-binding subunit M / Ketone dehydrogenase medium FAD subunit


Mass: 31469.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenarthrobacter nicotinovorans (bacteria)
Gene: kdhA, kdhM / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O87681, 6-hydroxypseudooxynicotine dehydrogenase
#3: Protein 6-hydroxypseudooxynicotine dehydrogenase complex subunit beta / / molybdopterin-binding subunit S / Ketone dehydrogenase small FeS subunit


Mass: 17660.904 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenarthrobacter nicotinovorans (bacteria)
Gene: kdhB, kdhS / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O87682, 6-hydroxypseudooxynicotine dehydrogenase
#4: Protein 6-hydroxypseudooxynicotine dehydrogenase complex subunit alpha / / molybdopterin-binding subunit M / Ketone dehydrogenase medium FAD subunit


Mass: 31469.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenarthrobacter nicotinovorans (bacteria)
Gene: kdhA, kdhM / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O87681, 6-hydroxypseudooxynicotine dehydrogenase

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Non-polymers , 4 types, 10 molecules

#5: Chemical ChemComp-MCN / PTERIN CYTOSINE DINUCLEOTIDE


Mass: 696.501 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H22N8O13P2S2
#6: Chemical ChemComp-MO / MOLYBDENUM ATOM


Mass: 95.940 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mo
#7: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#8: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2

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Details

Has ligand of interestN

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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: 3.94 Å3/Da / Density % sol: 68.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 4000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Dec 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.43→147.24 Å / Num. obs: 56814 / % possible obs: 96 % / Redundancy: 12.2 % / CC1/2: 0.87 / Net I/σ(I): 1.1
Reflection shellResolution: 3.43→3.55 Å / Num. unique obs: 5553 / CC1/2: 0.512

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 3.44→147.24 Å / Cor.coef. Fo:Fc: 0.844 / Cor.coef. Fo:Fc free: 0.791 / SU B: 88.643 / SU ML: 0.625 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.709 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.326 2706 5.1 %RANDOM
Rwork0.2875 ---
obs0.2894 50560 93.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 153.74 Å2 / Biso mean: 67.87 Å2 / Biso min: 31.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2---0.78 Å20 Å2
3---0.86 Å2
Refinement stepCycle: final / Resolution: 3.44→147.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18466 0 212 0 18678
Biso mean--65.27 --
Num. residues----2435
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01919055
X-RAY DIFFRACTIONr_angle_refined_deg1.3881.97425902
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.89552428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.89123.604838
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.986153039
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.89515159
X-RAY DIFFRACTIONr_chiral_restr0.0970.22968
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02114479
X-RAY DIFFRACTIONr_rigid_bond_restr3.928319055
X-RAY DIFFRACTIONr_sphericity_bonded2.615518676
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A6790.26
12D6790.26
21B2920.26
22E2920.26
31C2400.13
32F2400.13
LS refinement shellResolution: 3.443→3.532 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 124 -
Rwork0.346 2153 -
all-2277 -
obs--55.01 %

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