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- PDB-8gob: Crystal Structure of Glycerol Dehydrogenase in the presence of NAD+ -

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Basic information

Entry
Database: PDB / ID: 8gob
TitleCrystal Structure of Glycerol Dehydrogenase in the presence of NAD+
ComponentsGlycerol dehydrogenase
KeywordsOXIDOREDUCTASE / Glycerol dehydrogenase / complex
Function / homology
Function and homology information


(R)-aminopropanol dehydrogenase / (R)-aminopropanol dehydrogenase activity / anaerobic glycerol catabolic process / methylglyoxal catabolic process / glycerol dehydrogenase / glycerol dehydrogenase (NAD+) activity / protein homotetramerization / protein-containing complex / zinc ion binding / identical protein binding / cytosol
Similarity search - Function
Glycerol dehydrogenase / Iron-containing alcohol dehydrogenases signature 2. / Iron-containing alcohol dehydrogenases signature 1. / Alcohol dehydrogenase, iron-type, conserved site / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glycerol dehydrogenase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsPark, T. / Hoang, H.N. / Kang, J.Y. / Park, J. / Mun, S.A. / Jin, M. / Yang, J. / Jung, C.-H. / Eom, S.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2021R1A2C1006267 Korea, Republic Of
CitationJournal: Febs J. / Year: 2023
Title: Structural and functional insights into the flexible beta-hairpin of glycerol dehydrogenase.
Authors: Park, T. / Hoang, H.N. / Kang, J.Y. / Park, J. / Mun, S.A. / Jin, M. / Yang, J. / Jung, C.H. / Eom, S.H.
History
DepositionAug 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycerol dehydrogenase
B: Glycerol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4589
Polymers79,6342
Non-polymers1,8247
Water6,035335
1
A: Glycerol dehydrogenase
B: Glycerol dehydrogenase
hetero molecules

A: Glycerol dehydrogenase
B: Glycerol dehydrogenase
hetero molecules

A: Glycerol dehydrogenase
B: Glycerol dehydrogenase
hetero molecules

A: Glycerol dehydrogenase
B: Glycerol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)325,83436
Polymers318,5378
Non-polymers7,29628
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area34040 Å2
ΔGint-402 kcal/mol
Surface area94680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.878, 129.878, 266.214
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-654-

HOH

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Components

#1: Protein Glycerol dehydrogenase / GDH / GLDH / (R)-aminopropanol dehydrogenase / 1 / 2-propanediol dehydrogenase / D-1-amino-2- ...GDH / GLDH / (R)-aminopropanol dehydrogenase / 1 / 2-propanediol dehydrogenase / D-1-amino-2-propanol oxidoreductase


Mass: 39817.152 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: gldA, b3945, JW5556 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0A9S5, glycerol dehydrogenase, (R)-aminopropanol dehydrogenase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 3.62 Å3/Da / Density % sol: 66.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM Na2HPO4-citrate (pH 4.2), 200 mM NaCl, and 10% (w/v) PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.6→49.3 Å / Num. obs: 34920 / % possible obs: 99.1 % / Redundancy: 8.7 % / Net I/σ(I): 8.8
Reflection shellResolution: 2.6→2.72 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZXL

5zxl


Resolution: 2.6→48.6 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1786 5.12 %RANDOM
Rwork0.186 ---
obs0.188 34890 98.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→48.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5410 0 114 335 5859
LS refinement shellResolution: 2.6→2.67 Å
RfactorNum. reflection% reflection
Rfree0.3606 131 -
Rwork0.3066 2416 -
obs--96 %

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