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- PDB-8ij7: Crystal structure of alcohol dehydrogenase from Burkholderia gladioli -

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Basic information

Entry
Database: PDB / ID: 8ij7
TitleCrystal structure of alcohol dehydrogenase from Burkholderia gladioli
ComponentsPutative short-chain dehydrogenases/reductase family protein
KeywordsOXIDOREDUCTASE / alcohol dehydrogenase / wild type
Function / homologyPKS_KR / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / nucleotide binding / Putative short-chain dehydrogenases/reductase family protein
Function and homology information
Biological speciesBurkholderia gladioli (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsHan, X. / Mei, Z.L. / Liu, W.D. / Sun, Z.T. / Ma, J.A.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of alcohol dehydrogenase from Burkholderia gladioli
Authors: Han, X. / Mei, Z.L. / Liu, W.D. / Sun, Z.T. / Ma, J.A.
History
DepositionFeb 26, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative short-chain dehydrogenases/reductase family protein
B: Putative short-chain dehydrogenases/reductase family protein
C: Putative short-chain dehydrogenases/reductase family protein
D: Putative short-chain dehydrogenases/reductase family protein


Theoretical massNumber of molelcules
Total (without water)103,5254
Polymers103,5254
Non-polymers00
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11940 Å2
ΔGint-84 kcal/mol
Surface area34710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.402, 109.407, 217.463
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Putative short-chain dehydrogenases/reductase family protein


Mass: 25881.197 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia gladioli (strain BSR3) (bacteria)
Gene: bgla_2g00620 / Production host: Escherichia coli (E. coli) / References: UniProt: F2LIG4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60.5 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop
Details: 18% MPD, 18% PEG1000, 18% PEG3350, 0.1M HEPES, pH7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.54→27.35 Å / Num. obs: 40594 / % possible obs: 94.52 % / Redundancy: 10.8 % / CC1/2: 0.98 / Net I/σ(I): 16.9
Reflection shellResolution: 2.54→2.65 Å / Num. unique obs: 40594 / CC1/2: 0.98

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.54→27.35 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 34.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2944 2037 5.02 %
Rwork0.2464 --
obs0.2488 40594 94.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.54→27.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7071 0 0 77 7148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d11.8181065
X-RAY DIFFRACTIONf_chiral_restr0.1051181
X-RAY DIFFRACTIONf_plane_restr0.0331301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.54-2.630.38041700.34033195X-RAY DIFFRACTION80
2.63-2.740.39982010.32633778X-RAY DIFFRACTION93
2.74-2.860.37381940.31723811X-RAY DIFFRACTION94
2.86-3.010.37922040.30923798X-RAY DIFFRACTION95
3.01-3.20.33682060.29643891X-RAY DIFFRACTION95
3.2-3.450.3252020.28083844X-RAY DIFFRACTION95
3.45-3.790.32552050.25693940X-RAY DIFFRACTION97
3.79-4.340.28182190.23383998X-RAY DIFFRACTION98
4.34-5.460.24872190.22034085X-RAY DIFFRACTION99
5.46-27.350.25182170.2024217X-RAY DIFFRACTION99

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