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- PDB-8k1h: Crystal structure of ethylene glycol-bound glycerol dehydrogenase... -

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Basic information

Entry
Database: PDB / ID: 8k1h
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / L(+)-TARTARIC ACID / Glycerol dehydrogenase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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)39,9377
Polymers38,7841
Non-polymers1,1536
Water4,576254
1
A: Glycerol dehydrogenase
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)319,49856
Polymers310,2738
Non-polymers9,22548
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 area39920 Å2
ΔGint-424 kcal/mol
Surface area92130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.732, 179.732, 84.923
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

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 260 molecules

#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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.42 Å3/Da / Density % sol: 72.18 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.6 M ammonium tartrate dibasic, 0.15 M sodium acetate trihydrate(pH4.6)

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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: Nov 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 40658 / % possible obs: 100 % / Redundancy: 17.6 % / Biso Wilson estimate: 29.45 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.153 / Net I/σ(I): 49.5
Reflection shellResolution: 2.1→2.14 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2023 / CC1/2: 0.88 / Rrim(I) all: 0.91

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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: 2.1→48.95 Å / SU ML: 0.1939 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.6515
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1917 1999 4.92 %
Rwork0.1697 38625 -
obs0.1708 40624 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.67 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2695 0 73 254 3022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00742819
X-RAY DIFFRACTIONf_angle_d0.97533840
X-RAY DIFFRACTIONf_chiral_restr0.0546450
X-RAY DIFFRACTIONf_plane_restr0.0081496
X-RAY DIFFRACTIONf_dihedral_angle_d10.7891398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.25041390.20762687X-RAY DIFFRACTION98.64
2.15-2.210.27061410.19852724X-RAY DIFFRACTION100
2.21-2.280.26861420.1862745X-RAY DIFFRACTION99.97
2.28-2.350.24531400.18572715X-RAY DIFFRACTION100
2.35-2.430.19941420.18672740X-RAY DIFFRACTION100
2.43-2.530.23561420.18662730X-RAY DIFFRACTION100
2.53-2.650.16421410.17692739X-RAY DIFFRACTION99.97
2.65-2.780.22961420.17522740X-RAY DIFFRACTION100
2.79-2.960.21951420.18492750X-RAY DIFFRACTION100
2.96-3.190.23771430.19042755X-RAY DIFFRACTION99.97
3.19-3.510.19321430.1722771X-RAY DIFFRACTION100
3.51-4.020.1581440.15832777X-RAY DIFFRACTION100
4.02-5.060.14561460.13412833X-RAY DIFFRACTION100
5.06-48.950.16261520.16152919X-RAY DIFFRACTION99.03
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)
11.02263977028-0.117223348548-0.3006934360931.204383708411.189363870882.190661365590.07778979097340.00794686227341-0.0646810238483-0.08962064766380.0823807364406-0.1023894933060.11537719558-0.00890095843492-0.1611757465430.250387358389-0.039035846521-0.02071396357790.1822356506730.01378719324510.24721371525-27.4562812876-35.5674567551-7.57790536477
22.092146732710.7216914825990.09127582617972.53398773160.3127160020041.87068743393-0.06160023796960.1380701928220.0361465070485-0.1825248089930.03572766326090.1968096912060.0418783770907-0.1854612175340.03590354708060.269664039676-0.0709135740521-0.05820609383290.231210689109-0.03170119754970.264584745137-34.9483903862-36.7785624347-16.970510208
30.7945043013-0.222900566083-0.3072954439981.339678374770.3419714090760.999560774750.006968703346590.125735754703-0.0928652989875-0.131756144939-0.01428728380980.18877748591-0.0183893639214-0.04915056424820.0002915655122220.22318765679-0.0294967995712-0.05088236103250.211786116069-0.02155728399390.213688230218-23.9157683338-20.4338896984-12.3122550086
42.09869545759-0.85434259337-0.01890906427832.96102757621-0.3993514652861.920252923220.09120735223460.283239185784-0.0779155310498-0.450207013172-0.08565391754950.2871139275880.00631123160342-0.1632595605140.002634165244910.275716312910.00388053495956-0.08349844453180.253046410682-0.026307151930.195768646695-28.0671678607-5.08348436677-22.2033704033
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 37 )1 - 371 - 37
22chain 'A' and (resid 38 through 131 )38 - 13138 - 131
33chain 'A' and (resid 132 through 248 )132 - 248132 - 248
44chain 'A' and (resid 249 through 367 )249 - 367249 - 367

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