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- PDB-8ijg: Crystal structure of alcohol dehydrogenase M5 from Burkholderia g... -

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Basic information

Entry
Database: PDB / ID: 8ijg
TitleCrystal structure of alcohol dehydrogenase M5 from Burkholderia gladioli with NADP
ComponentsPutative short-chain dehydrogenases/reductase family protein
KeywordsOXIDOREDUCTASE / alcohol dehydrogenase
Function / homology: / 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 BSR3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 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 27, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)106,7318
Polymers103,7574
Non-polymers2,9744
Water4,954275
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17000 Å2
ΔGint-96 kcal/mol
Surface area33190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.127, 111.050, 229.917
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: 25939.297 Da / Num. of mol.: 4 / Mutation: V84I,G92A,S138A,A140K,L203T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia gladioli BSR3 (bacteria) / Gene: bgla_2g00620
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
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: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 3.3 Å3/Da / Density % sol: 62.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES, pH6.5, 12% PEG 500 MME, 6% PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.988 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 2.27→73 Å / Num. obs: 63273 / % possible obs: 99.5 % / Redundancy: 13.9 % / CC1/2: 0.999 / Net I/σ(I): 18.6
Reflection shellResolution: 2.27→2.39 Å / Mean I/σ(I) obs: 2.8 / Num. unique obs: 9070 / CC1/2: 0.895 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.2refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.27→48.55 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2536 3131 4.97 %
Rwork0.2202 --
obs0.2219 63058 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.27→48.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7203 0 192 275 7670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097528
X-RAY DIFFRACTIONf_angle_d1.28410216
X-RAY DIFFRACTIONf_dihedral_angle_d11.8731224
X-RAY DIFFRACTIONf_chiral_restr0.0671228
X-RAY DIFFRACTIONf_plane_restr0.0221316
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.350.35023070.29785875X-RAY DIFFRACTION99
2.35-2.450.33953060.28135912X-RAY DIFFRACTION99
2.45-2.560.30543030.27365931X-RAY DIFFRACTION99
2.56-2.690.31693160.26955952X-RAY DIFFRACTION99
2.69-2.860.30453090.25745969X-RAY DIFFRACTION99
2.86-3.080.28973080.25885975X-RAY DIFFRACTION99
3.08-3.390.3033150.25715973X-RAY DIFFRACTION99
3.39-3.880.26123110.2296032X-RAY DIFFRACTION99
3.88-4.890.21243230.18436070X-RAY DIFFRACTION100
4.89-48.550.18443330.16376238X-RAY DIFFRACTION99

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