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- PDB-8ij6: Crystal structure of alcohol dehydrogenase from Burkholderia glad... -

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Basic information

Entry
Database: PDB / ID: 8ij6
TitleCrystal structure of alcohol dehydrogenase from Burkholderia gladioli with NADP
ComponentsPutative short-chain dehydrogenases/reductase family protein
KeywordsOXIDOREDUCTASE / alcohol dehydrogenase
Function / homologyoxidoreductase activity, acting on NAD(P)H, oxygen as acceptor / PKS_KR / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / nucleotide binding / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Putative short-chain dehydrogenases/reductase family protein
Function and homology information
Biological speciesBurkholderia gladioli (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 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 with NADP
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,4988
Polymers103,5254
Non-polymers2,9744
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17150 Å2
ΔGint-93 kcal/mol
Surface area32730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.830, 109.590, 215.768
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: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O
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: 3.05 Å3/Da / Density % sol: 59.7 %
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: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.28→53.43 Å / Num. obs: 56690 / % possible obs: 98.02 % / Redundancy: 104 % / CC1/2: 0.997 / Net I/σ(I): 1.34
Reflection shellResolution: 2.28→2.41 Å / Num. unique obs: 56690 / CC1/2: 0.773

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Processing

Software
NameVersionClassification
XDSdata scaling
REFMAC5.8.0123refinement
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→53.42 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2396 2836 5 %
Rwork0.2006 --
obs0.2025 56690 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.28→53.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7202 0 192 269 7663
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d10.7091224
X-RAY DIFFRACTIONf_chiral_restr0.0631224
X-RAY DIFFRACTIONf_plane_restr0.0121316
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.360.30492860.26475434X-RAY DIFFRACTION100
2.36-2.460.28092800.24575427X-RAY DIFFRACTION100
2.46-2.570.30072910.24915438X-RAY DIFFRACTION100
2.57-2.710.30372300.24894366X-RAY DIFFRACTION80
2.71-2.880.272860.22265466X-RAY DIFFRACTION100
2.88-3.10.2532840.22865477X-RAY DIFFRACTION100
3.1-3.410.25223000.22525456X-RAY DIFFRACTION100
3.41-3.90.23912850.20055518X-RAY DIFFRACTION100
3.9-4.920.20052900.16555549X-RAY DIFFRACTION100
4.92-53.420.21333040.16895723X-RAY DIFFRACTION100

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