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- PDB-1r59: Enterococcus casseliflavus glycerol kinase -

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Basic information

Entry
Database: PDB / ID: 1r59
TitleEnterococcus casseliflavus glycerol kinase
ComponentsGlycerol kinase
KeywordsTRANSFERASE
Function / homology
Function and homology information


glycerol kinase / glycerol kinase activity / glycerol-3-phosphate metabolic process / glycerol metabolic process / glycerol catabolic process / phosphorylation / ATP binding
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 / MIR / Resolution: 2.5 Å
AuthorsYeh, J.I. / Charrier, V. / Paulo, J. / Hou, L. / Darbon, E. / Claiborne, A. / Hol, W.G. / Deutscher, J.
CitationJournal: Biochemistry / Year: 2004
Title: Structures of Enterococcal Glycerol Kinase in the Absence and Presence of Glycerol: Correlation of conformation to substrate binding and a mechanism of activation by phosphorylation
Authors: Yeh, J.I. / Charrier, V. / Paulo, J. / Hou, L. / Darbon, E. / Claiborne, A. / Hol, W.G. / Deutscher, J.
History
DepositionOct 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
O: Glycerol kinase
X: Glycerol kinase


Theoretical massNumber of molelcules
Total (without water)111,3632
Polymers111,3632
Non-polymers00
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.829, 107.110, 201.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 55681.293 Da / Num. of mol.: 2 / Fragment: Glycerol kinase
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): JM109DE3 / References: UniProt: O34153, glycerol kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 3

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Sample preparation

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 62.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: PEG400, potassium phosphate, 1,10-phenanthroline, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9788, 0.9791, 0.954, 1.0
DetectorType: ADSC QUANTUM 4 / Detector: CCD
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1graphiteSINGLE WAVELENGTHMx-ray1
2graphiteMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97881
20.97911
30.9541
411
ReflectionResolution: 2.5→50 Å / Num. obs: 40746 / % possible obs: 95.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.072 / Rsym value: 0.045 / Net I/σ(I): 9.7
Reflection shellResolution: 2.5→2.61 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 5.4 / Num. unique all: 29592 / Rsym value: 0.27 / % possible all: 74.7

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MIR / Resolution: 2.5→6 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
Details: Residue (O SER 230 ) and Residue (O VAL 238 ) are linked together. Residue (X SER 230 ) and Residue (X VAL 238 ) are linked togethe.
RfactorNum. reflectionSelection details
Rfree0.243 -random
Rwork0.221 --
all-40746 -
obs-29592 -
Displacement parametersBiso mean: 34.7 Å2
Refine analyzeLuzzati sigma a obs: 0.1 Å
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7430 0 0 102 7532
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.007
X-RAY DIFFRACTIONr_angle_refined_deg2.2

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