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- PDB-8x6m: Crystal Structure of Glycerol Dehydrogenase in the Presence of NA... -

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Basic information

Entry
Database: PDB / ID: 8x6m
TitleCrystal Structure of Glycerol Dehydrogenase in the Presence of NAD+ and Glycerol
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 Å
AuthorsPark, T. / Kang, J.Y. / Jin, M. / Yang, J. / Kim, H. / Noh, C. / Eom, S.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2021R1A2C1006267 Korea, Republic Of
CitationJournal: Plos One / Year: 2024
Title: Structural insights into the octamerization of glycerol dehydrogenase.
Authors: Park, T. / Kang, J.Y. / Jin, M. / Yang, J. / Kim, H. / Noh, C. / Jung, C.H. / Eom, S.H.
History
DepositionNov 21, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)81,2768
Polymers79,6342
Non-polymers1,6426
Water7,728429
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)325,10532
Polymers318,5378
Non-polymers6,56724
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-y-1,x,z1
crystal symmetry operation4_545y,-x-1,z1
Buried area31140 Å2
ΔGint-461 kcal/mol
Surface area97010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.893, 131.893, 265.259
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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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) / 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: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 0.97942 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2→118.1 Å / Num. obs: 78784 / % possible obs: 99.9 % / Redundancy: 26.1 % / CC1/2: 0.999 / Net I/σ(I): 19
Reflection shellResolution: 2→2 Å / Num. unique obs: 3865 / CC1/2: 0.94 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8GOB

8gob


Resolution: 2→50.01 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.869 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20952 4016 5.1 %RANDOM
Rwork0.1756 ---
obs0.17736 74751 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.575 Å2
Baniso -1Baniso -2Baniso -3
1-1.43 Å2-0 Å2-0 Å2
2--1.43 Å20 Å2
3----2.86 Å2
Refinement stepCycle: 1 / Resolution: 2→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5438 0 102 429 5969
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125651
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165352
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.6487705
X-RAY DIFFRACTIONr_angle_other_deg0.5241.56612325
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1125734
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.428526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.68110875
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0750.2903
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026624
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021182
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.223.4622939
X-RAY DIFFRACTIONr_mcbond_other3.2193.4622939
X-RAY DIFFRACTIONr_mcangle_it4.3096.2053672
X-RAY DIFFRACTIONr_mcangle_other4.3096.2073673
X-RAY DIFFRACTIONr_scbond_it5.324.2332712
X-RAY DIFFRACTIONr_scbond_other5.3224.2332713
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.1727.5084034
X-RAY DIFFRACTIONr_long_range_B_refined9.03235.426534
X-RAY DIFFRACTIONr_long_range_B_other9.03534.496420
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 314 -
Rwork0.262 5409 -
obs--99.55 %

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