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- PDB-8goa: Crystal Structure of Glycerol Dehydrogenase in the absence of NAD+ -

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Basic information

Entry
Database: PDB / ID: 8goa
TitleCrystal Structure of Glycerol Dehydrogenase in the absence 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
Glycerol dehydrogenase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)160,99620
Polymers159,2694
Non-polymers1,72716
Water6,828379
1
A: Glycerol dehydrogenase
B: Glycerol dehydrogenase
C: Glycerol dehydrogenase
D: Glycerol dehydrogenase
hetero molecules

A: Glycerol dehydrogenase
B: Glycerol dehydrogenase
C: Glycerol dehydrogenase
D: Glycerol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)321,99240
Polymers318,5378
Non-polymers3,45532
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area28220 Å2
ΔGint-304 kcal/mol
Surface area98770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.470, 161.470, 291.907
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Glycerol dehydrogenase / GDH / GLDH


Mass: 39817.152 Da / Num. of mol.: 4
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
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 5.97 Å3/Da / Density % sol: 79.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium citrate (pH 5.6), 500 mM ammonium sulfate, and 1 M lithium sulfate

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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: 2.9→49.24 Å / Num. obs: 86081 / % possible obs: 99.6 % / Redundancy: 8.7 % / CC1/2: 0.99 / Net I/σ(I): 6.8
Reflection shellResolution: 2.9→2.95 Å / Num. unique obs: 4204 / CC1/2: 0.322

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5zxl

5zxl


Resolution: 2.9→49.24 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2199 4362 5.08 %
Rwork0.1923 --
obs0.1937 85847 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→49.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10844 0 100 379 11323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811128
X-RAY DIFFRACTIONf_angle_d0.91415147
X-RAY DIFFRACTIONf_dihedral_angle_d6.9291588
X-RAY DIFFRACTIONf_chiral_restr0.0531760
X-RAY DIFFRACTIONf_plane_restr0.0061971
LS refinement shellResolution: 2.9→2.93 Å
RfactorNum. reflection% reflection
Rfree0.3855 140 -
Rwork0.3593 2598 -
obs--96 %

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