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- PDB-8ij8: Crystal structure of alcohol dehydrogenase M4 mutant from Burkhol... -

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Basic information

Entry
Database: PDB / ID: 8ij8
TitleCrystal structure of alcohol dehydrogenase M4 mutant from Burkholderia gladioli
ComponentsPutative short-chain dehydrogenases/reductase family protein
KeywordsOXIDOREDUCTASE / alcohol dehydrogenase
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: 2.38 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 M4 mutant 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
E: Putative short-chain dehydrogenases/reductase family protein
F: Putative short-chain dehydrogenases/reductase family protein
G: Putative short-chain dehydrogenases/reductase family protein
H: Putative short-chain dehydrogenases/reductase family protein


Theoretical massNumber of molelcules
Total (without water)207,6428
Polymers207,6428
Non-polymers00
Water6,936385
1
A: Putative short-chain dehydrogenases/reductase family protein
C: Putative short-chain dehydrogenases/reductase family protein
D: Putative short-chain dehydrogenases/reductase family protein
F: Putative short-chain dehydrogenases/reductase family protein


Theoretical massNumber of molelcules
Total (without water)103,8214
Polymers103,8214
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11980 Å2
ΔGint-84 kcal/mol
Surface area34740 Å2
MethodPISA
2
B: Putative short-chain dehydrogenases/reductase family protein
E: Putative short-chain dehydrogenases/reductase family protein
G: Putative short-chain dehydrogenases/reductase family protein
H: Putative short-chain dehydrogenases/reductase family protein


Theoretical massNumber of molelcules
Total (without water)103,8214
Polymers103,8214
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12090 Å2
ΔGint-81 kcal/mol
Surface area33920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.305, 141.305, 164.757
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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Components

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


Mass: 25955.297 Da / Num. of mol.: 8 / Mutation: V84I,G92A,A140K,L203T
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.: 385 / 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: 3.96 Å3/Da / Density % sol: 68.95 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M MES, pH 6.5, 2.0M Sodium Chloride, 0.1M Sodium dihydrogen phosphate mono, 0.1M mono-Potassium dihydrogen Phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.38→141.3 Å / Num. obs: 127246 / % possible obs: 98.1 % / Redundancy: 15.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.045 / Rrim(I) all: 0.177 / Χ2: 1.01 / Net I/σ(I): 15.3 / Num. measured all: 1927359
Reflection shellResolution: 2.38→2.51 Å / Rmerge(I) obs: 1.532 / Num. unique obs: 18882 / CC1/2: 0.802 / Rpim(I) all: 0.403 / Χ2: 0.97

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Processing

Software
NameVersionClassification
HKL-3000data scaling
HKL-3000data reduction
PHENIX1.1932-4158refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→49.96 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 0.92 / Phase error: 30.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2576 6312 4.99 %
Rwork0.2253 --
obs0.227 126559 97.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.38→49.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14181 0 0 385 14566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d13.3852132
X-RAY DIFFRACTIONf_chiral_restr0.1392372
X-RAY DIFFRACTIONf_plane_restr0.0332604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.470.37226410.334912225X-RAY DIFFRACTION100
2.47-2.560.35396420.313412236X-RAY DIFFRACTION100
2.56-2.660.33935280.296510129X-RAY DIFFRACTION98
2.68-2.820.32716260.281411958X-RAY DIFFRACTION100
2.82-30.32956370.27412229X-RAY DIFFRACTION100
3-3.230.29886470.26212237X-RAY DIFFRACTION100
3.23-3.550.26146460.237512276X-RAY DIFFRACTION100
3.56-4.070.24246510.208412252X-RAY DIFFRACTION100
4.07-5.130.20476440.173812315X-RAY DIFFRACTION100
5.13-49.960.19936500.181212390X-RAY DIFFRACTION100

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