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- PDB-7wmk: PQQ-dependent alcohol dehydrogenase complexed with PQQ -

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Basic information

Entry
Database: PDB / ID: 7wmk
TitlePQQ-dependent alcohol dehydrogenase complexed with PQQ
ComponentsPQQ-dependent alcohol dehydrogenase
KeywordsTOXIN / dehydrogenase / PQQ
Function / homologyACETATE ION / PYRROLOQUINOLINE QUINONE
Function and homology information
Biological speciesDevosia albogilva (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsChen, M. / Yang, H. / Lv, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32000889 China
CitationJournal: J.Agric.Food Chem. / Year: 2022
Title: Structure-Function Analysis of a Quinone-Dependent Dehydrogenase Capable of Deoxynivalenol Detoxification.
Authors: Yang, H. / Yan, R. / Li, Y. / Lu, Z. / Bie, X. / Zhao, H. / Lu, F. / Chen, M.
History
DepositionJan 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PQQ-dependent alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,80911
Polymers61,9081
Non-polymers90110
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-19 kcal/mol
Surface area18980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.973, 91.190, 57.332
Angle α, β, γ (deg.)90.000, 103.780, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-822-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PQQ-dependent alcohol dehydrogenase


Mass: 61908.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Devosia albogilva (bacteria) / Production host: Escherichia coli (E. coli)

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Non-polymers , 7 types, 325 molecules

#2: Chemical ChemComp-PQQ / PYRROLOQUINOLINE QUINONE


Mass: 330.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H6N2O8 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.26 Å3/Da / Density % sol: 45.47 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 250mM Sodium acetate, 100mM BIS-Tris (pH 7.5), 150mM NaCl, 15% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.47→47.25 Å / Num. obs: 95115 / % possible obs: 98.7 % / Redundancy: 6.6 % / CC1/2: 0.998 / Net I/σ(I): 14.16
Reflection shellResolution: 1.47→1.54 Å / Num. unique obs: 15196 / CC1/2: 0.894

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7WMD

7wmd


Resolution: 1.47→44.151 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 12.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1401 2000 2.15 %
Rwork0.1384 91081 -
obs0.1385 93081 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.9 Å2 / Biso mean: 21.9791 Å2 / Biso min: 0.69 Å2
Refinement stepCycle: final / Resolution: 1.47→44.151 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4184 0 79 315 4578
Biso mean--28.67 28.58 -
Num. residues----557
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.47-1.50680.22021420.22886487
1.5068-1.54750.22631430.19066497
1.5475-1.5930.15791430.16186481
1.593-1.64450.15341400.15236438
1.6445-1.70320.13431450.13016526
1.7032-1.77140.12471410.12326485
1.7714-1.85210.13831440.12556506
1.8521-1.94970.13891420.12516475
1.9497-2.07190.1251430.12216547
2.0719-2.23180.12661430.12246489
2.2318-2.45640.11971420.12816476
2.4564-2.81180.141440.13726529
2.8118-3.54230.13531430.13966543
3.5423-44.1510.14771450.14636602

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