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- PDB-9m2k: Type I PQQ-dependent alcohol dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 9m2k
TitleType I PQQ-dependent alcohol dehydrogenase
ComponentsPQQ-binding-like beta-propeller repeat protein
KeywordsTOXIN / deoxynivalenol / dehydrogenase
Function / homologyGlucose/ethanol/alcohol dehydrogenase, beta-propeller domain / Pyrrolo-quinoline quinone repeat / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / Quinoprotein alcohol dehydrogenase-like superfamily / oxidoreductase activity / Chem-B2S / PYRROLOQUINOLINE QUINONE / PQQ-binding-like beta-propeller repeat protein
Function and homology information
Biological speciesParadevosia tibetensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsShi, Y. / Mu, W.M. / Xu, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22408125 China
CitationJournal: To Be Published
Title: PQQ-dependent dehydrogenase able to detoxify DON
Authors: Shi, Y. / Mu, W.M. / Xu, W.
History
DepositionFeb 27, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PQQ-binding-like beta-propeller repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8844
Polymers64,2171
Non-polymers6673
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-21 kcal/mol
Surface area18170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.454, 94.883, 58.461
Angle α, β, γ (deg.)90.00, 105.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PQQ-binding-like beta-propeller repeat protein


Mass: 64217.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paradevosia tibetensis (bacteria) / Gene: FNA67_03370 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5B9DJI2
#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-B2S / (3alpha,7alpha)-3,7,15-trihydroxy-12,13-epoxytrichothec-9-en-8-one


Mass: 296.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C15H20O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG400, Imidazole, PEGMME5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: May 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.15→38.92 Å / Num. obs: 25718 / % possible obs: 99.8 % / Redundancy: 8 % / CC1/2: 0.981 / Net I/σ(I): 6.2
Reflection shellResolution: 2.63→2.76 Å / Num. unique obs: 2247 / CC1/2: 0.862

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
APEXdata reduction
APEXdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.63→23.35 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.889 / SU B: 33.06 / SU ML: 0.312 / Cross valid method: THROUGHOUT / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25468 847 5 %RANDOM
Rwork0.20478 ---
obs0.2073 16044 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.471 Å2
Baniso -1Baniso -2Baniso -3
1--1.79 Å2-0 Å22.95 Å2
2---4.09 Å20 Å2
3---3.76 Å2
Refinement stepCycle: 1 / Resolution: 2.63→23.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4222 0 46 30 4298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.024384
X-RAY DIFFRACTIONr_bond_other_d0.0010.023950
X-RAY DIFFRACTIONr_angle_refined_deg1.281.955994
X-RAY DIFFRACTIONr_angle_other_deg0.7739085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7725557
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.88424.607191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55315632
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7671521
X-RAY DIFFRACTIONr_chiral_restr0.0720.2651
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215090
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021005
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_it0.2642.0612231
X-RAY DIFFRACTIONr_mcbond_other0.2642.0612230
X-RAY DIFFRACTIONr_mcangle_it0.4653.0912787
X-RAY DIFFRACTIONr_mcangle_other0.4653.0912788
X-RAY DIFFRACTIONr_scbond_it0.2332.1152152
X-RAY DIFFRACTIONr_scbond_other0.2332.1172153
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.4083.1723205
X-RAY DIFFRACTIONr_long_range_B_refined1.32624.1454997
X-RAY DIFFRACTIONr_long_range_B_other1.32324.1554997
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.63→2.698 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 60 -
Rwork0.305 1174 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.99211.24630.53064.1108-0.70650.6896-0.0357-0.25470.41630.09660.01390.1008-0.0957-0.03810.02180.03270.00590.01990.0755-0.13030.266823.34726.264532.636
22.1105-0.28070.27120.0962-0.07321.7875-0.0719-0.27010.43460.0167-0.0066-0.0971-0.00630.00250.07850.0437-0.02410.04320.0799-0.07240.211835.529815.905435.6937
32.3259-0.4473-0.03542.84940.88483.15260.117-0.50050.16530.27110.05530.02570.1620.2166-0.17230.0921-0.03840.05620.1348-0.05570.076425.38532.955335.7829
41.5603-0.58260.33761.23870.15111.88190.1189-0.19120.12130.1087-0.07640.22690.1216-0.2914-0.04250.0671-0.04220.0770.0711-0.03370.127612.7752.504224.0507
50.82730.2260.64911.09970.0270.66410.01840.07080.2508-0.2254-0.11220.01050.043-0.00430.09380.08820.01430.05890.080.07320.198415.421312.47279.1104
61.3199-0.24940.49050.75070.15520.6992-0.02590.26270.6041-0.1064-0.119-0.0239-0.09420.00430.14490.10050.00740.05870.07050.12390.384232.45823.402211.9041
72.2446-0.03350.36580.3379-0.76961.79410.0114-0.0010.45070.0039-0.04010.0046-0.02370.09460.02870.0684-0.00130.08490.00740.00960.257638.360818.493923.49
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 82
2X-RAY DIFFRACTION2A83 - 134
3X-RAY DIFFRACTION3A135 - 185
4X-RAY DIFFRACTION4A186 - 279
5X-RAY DIFFRACTION5A280 - 471
6X-RAY DIFFRACTION6A472 - 544
7X-RAY DIFFRACTION7A545 - 600

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