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- PDB-9jx4: Crystal Structure of an aldehyde-alcohol dehydrogenase in complex... -

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Basic information

Entry
Database: PDB / ID: 9jx4
TitleCrystal Structure of an aldehyde-alcohol dehydrogenase in complex with metformin
ComponentsAldehyde-alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / aldehyde alcohol dehydrogenase / metal ion binding
Function / homology
Function and homology information


alcohol dehydrogenase (NAD+) activity / metal ion binding
Similarity search - Function
Iron-type alcohol dehydrogenase-like / : / Fe-containing alcohol dehydrogenase family, C-terminal / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase
Similarity search - Domain/homology
: / Metformin / Aldehyde-alcohol dehydrogenase
Similarity search - Component
Biological speciesAnaerobutyricum hallii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsXia, Y. / Yao, D. / Zhao, Y. / Cao, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82072468 China
CitationJournal: To Be Published
Title: Crystal Structure of an aldehyde-alcohol dehydrogenase in complex with metformin
Authors: Xia, Y. / Yao, D. / Zhao, Y. / Cao, Y.
History
DepositionOct 11, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aldehyde-alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1803
Polymers40,9951
Non-polymers1852
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.510, 98.510, 99.327
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Aldehyde-alcohol dehydrogenase


Mass: 40994.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anaerobutyricum hallii (bacteria) / Gene: adhE_1, ERS852450_01078 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A174BVF5
#2: Chemical ChemComp-MF8 / Metformin / N,N-Dimethylimidodicarbonimidic diamide


Mass: 129.164 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H11N5 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antipsychotic*YM
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.39 Å3/Da / Density % sol: 63.76 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG 6000, 100 mM Citric acid/ Sodium hydroxide pH 5.0

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 25787 / % possible obs: 89.97 % / Redundancy: 4.7 % / CC1/2: 0.915 / Net I/σ(I): 4.7
Reflection shellResolution: 2.2→2.24 Å / Num. unique obs: 1502 / CC1/2: 0.74

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.67 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0.49 / Phase error: 25.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2662 1959 7.6 %
Rwork0.2131 --
obs0.2171 25787 89.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→19.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2827 0 10 142 2979
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.887
X-RAY DIFFRACTIONf_dihedral_angle_d17.082
X-RAY DIFFRACTIONf_chiral_restr0.051
X-RAY DIFFRACTIONf_plane_restr0.007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.34341170.25141385X-RAY DIFFRACTION75
2.26-2.320.31421290.2311530X-RAY DIFFRACTION83
2.32-2.380.28421370.24161619X-RAY DIFFRACTION86
2.38-2.460.28531410.22391668X-RAY DIFFRACTION89
2.46-2.550.28081370.21931684X-RAY DIFFRACTION91
2.55-2.650.2591440.21941748X-RAY DIFFRACTION93
2.65-2.770.28121410.22561782X-RAY DIFFRACTION94
2.77-2.920.25931480.23011776X-RAY DIFFRACTION94
2.92-3.10.26591500.22451802X-RAY DIFFRACTION96
3.1-3.340.27431420.22631794X-RAY DIFFRACTION94
3.34-3.670.26081430.21471757X-RAY DIFFRACTION93
3.67-4.20.25671410.18451739X-RAY DIFFRACTION91
4.2-5.270.24141410.19091755X-RAY DIFFRACTION91
5.27-19.670.25831480.20781789X-RAY DIFFRACTION89

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