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- PDB-3h46: Glycerol Kinase H232E with Glycerol -

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Basic information

Entry
Database: PDB / ID: 3h46
TitleGlycerol Kinase H232E with Glycerol
ComponentsGlycerol kinase
KeywordsTRANSFERASE / glycerol / kinase / ATP-binding / Glycerol metabolism / Nucleotide-binding / Phosphoprotein
Function / homology
Function and homology information


glycerol-3-phosphate metabolic process / glycerol kinase / glycerol kinase activity / glycerol metabolic process / glycerol catabolic process / ATP binding / cytosol
Similarity search - Function
FGGY family of carbohydrate kinases signature 1. / Glycerol kinase / FGGY family of carbohydrate kinases signature 2. / Carbohydrate kinase, FGGY, conserved site / Carbohydrate kinase, FGGY / Carbohydrate kinase, FGGY, N-terminal / FGGY family of carbohydrate kinases, N-terminal domain / Carbohydrate kinase, FGGY, C-terminal / FGGY family of carbohydrate kinases, C-terminal domain / ATPase, nucleotide binding domain ...FGGY family of carbohydrate kinases signature 1. / Glycerol kinase / FGGY family of carbohydrate kinases signature 2. / Carbohydrate kinase, FGGY, conserved site / Carbohydrate kinase, FGGY / Carbohydrate kinase, FGGY, N-terminal / FGGY family of carbohydrate kinases, N-terminal domain / Carbohydrate kinase, FGGY, C-terminal / FGGY family of carbohydrate kinases, C-terminal domain / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEnterococcus casseliflavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsYeh, J.I. / Kettering, R.D.
CitationJournal: Biochemistry / Year: 2009
Title: Structural characterizations of glycerol kinase: unraveling phosphorylation-induced long-range activation
Authors: Yeh, J.I. / Kettering, R. / Saxl, R. / Bourand, A. / Darbon, E. / Joly, N. / Briozzo, P. / Deutscher, J.
History
DepositionApr 17, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Glycerol kinase
O: Glycerol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,1078
Polymers111,6072
Non-polymers5006
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
X: Glycerol kinase
O: Glycerol kinase
hetero molecules

X: Glycerol kinase
O: Glycerol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,21516
Polymers223,2144
Non-polymers1,00112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area12640 Å2
ΔGint-97 kcal/mol
Surface area67320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.677, 199.548, 56.813
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Glycerol kinase / ATP:glycerol 3-phosphotransferase / Glycerokinase / GK


Mass: 55803.453 Da / Num. of mol.: 2 / Mutation: H232E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus casseliflavus (bacteria) / Gene: glpK / Plasmid: pOXO4 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: O34153, glycerol kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O

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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: 2.46 Å3/Da / Density % sol: 49.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: HEPES, PEG 550 MME, ZnSO4, pH 6.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 16, 2007 / Details: mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 100197 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rsym value: 0.096 / Net I/σ(I): 8.4
Reflection shellResolution: 1.75→1.86 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.509 / % possible all: 81.4

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.005data extraction
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XUP

1xup


Resolution: 1.75→10 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 3
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.228 4004 5 %RANDOM
Rwork0.194 ---
all0.196 79736 --
obs0.196 75732 71.99 %-
Displacement parametersBiso max: 66.45 Å2 / Biso mean: 25.631 Å2 / Biso min: 10.72 Å2
Refinement stepCycle: LAST / Resolution: 1.75→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7758 0 30 193 7981
LS refinement shellResolution: 1.751→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 54 -
Rwork0.228 1155 -
all-1209 -
obs--15.33 %

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