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- PDB-8k1g: Crystal structure of ethylene glycol-bound glycerol dehydrogenase... -

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Basic information

Entry
Database: PDB / ID: 8k1g
TitleCrystal structure of ethylene glycol-bound glycerol dehydrogenase from Klebsiella pneumoniae
ComponentsGlycerol dehydrogenase
KeywordsOXIDOREDUCTASE / Glycerol Dehydrogenase / Ethylene Glycol
Function / homology
Function and homology information


glycerol dehydrogenase / glycerol dehydrogenase (NAD+) activity / glycerol catabolic process / generation of precursor metabolites and energy / nucleotide binding / metal ion 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 speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsKang, W.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2021R1A6A1A10044154 Korea, Republic Of
National Research Foundation (NRF, Korea)2022R1C1C1004221 Korea, Republic Of
CitationJournal: J. Korean Chem. Soc. / Year: 2024
Title: Crystal Structure of Glycerol Dehydrogenase from Klebsiella pneumoniae
Authors: Ko, G.S. / Nguyen, T.Q. / Kho, S. / Kang, W.
History
DepositionJul 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 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: Glycerol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2528
Polymers38,7841
Non-polymers4687
Water3,387188
1
A: Glycerol dehydrogenase
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)314,01664
Polymers310,2738
Non-polymers3,74356
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
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area31520 Å2
ΔGint-277 kcal/mol
Surface area96820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.014, 182.014, 80.707
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein Glycerol dehydrogenase


Mass: 38784.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: gldA / Production host: Escherichia coli (E. coli) / References: UniProt: A6TGD6, glycerol dehydrogenase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 4.31 Å3/Da / Density % sol: 71.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.6 M ammonium tartrate dibasic, 0.15 M sodium acetate tribasic

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 0 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 40012 / % possible obs: 100 % / Redundancy: 17.9 % / Biso Wilson estimate: 31.02 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.153 / Net I/σ(I): 19
Reflection shellResolution: 2.09→2.14 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1977 / CC1/2: 0.935 / Rrim(I) all: 0.934

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZXL

5zxl


Resolution: 2.09→48.5 Å / SU ML: 0.2092 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.5518
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2072 1976 4.94 %
Rwork0.1861 38030 -
obs0.1871 40006 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.1 Å2
Refinement stepCycle: LAST / Resolution: 2.09→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2695 0 27 188 2910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712767
X-RAY DIFFRACTIONf_angle_d0.89113754
X-RAY DIFFRACTIONf_chiral_restr0.0513438
X-RAY DIFFRACTIONf_plane_restr0.0063489
X-RAY DIFFRACTIONf_dihedral_angle_d5.9109398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.150.30021130.27242646X-RAY DIFFRACTION97.53
2.15-2.20.29721320.25432675X-RAY DIFFRACTION100
2.2-2.270.24451460.24152691X-RAY DIFFRACTION99.96
2.27-2.340.28351400.21852678X-RAY DIFFRACTION100
2.34-2.420.24221350.21342696X-RAY DIFFRACTION100
2.42-2.520.24691410.22022699X-RAY DIFFRACTION100
2.52-2.640.22981410.20742696X-RAY DIFFRACTION100
2.64-2.780.21871460.19612687X-RAY DIFFRACTION100
2.78-2.950.24821340.20272719X-RAY DIFFRACTION100
2.95-3.180.23451480.21132703X-RAY DIFFRACTION100
3.18-3.50.20581630.18342718X-RAY DIFFRACTION99.97
3.5-40.17541500.16422742X-RAY DIFFRACTION100
4-5.040.14021560.14322765X-RAY DIFFRACTION100
5.04-48.50.19191310.15592915X-RAY DIFFRACTION99.71
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8019207837720.6424914258410.4943428725851.963592301451.000700087521.88659770881-0.03536572135880.088841136449-0.0859572723307-0.1521662348050.0316677323470.2464795244070.0686620087469-0.1655488132980.008637136814740.226136435614-0.0470367555998-0.03483643091170.205531647717-0.01168647990480.302154776157-32.7421634363-35.4328500635-14.0999102589
20.823278632402-0.4544817275540.1605346817592.04784716117-0.1980130515851.12205741480.02334017599790.1244573838440.0266718714373-0.2227213297440.03849177054930.168809683482-0.0541123641319-0.111961300376-0.05235361571760.211751682434-0.0359037522577-0.0387521913630.225459375723-0.008892593794790.205239394268-25.0688200558-10.3691424191-17.4192475032
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 161 )1 - 1611 - 161
22chain 'A' and (resid 162 through 367 )162 - 367162 - 367

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