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- PDB-1xup: ENTEROCOCCUS CASSELIFLAVUS GLYCEROL KINASE COMPLEXED WITH GLYCEROL -

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Basic information

Entry
Database: PDB / ID: 1xup
TitleENTEROCOCCUS CASSELIFLAVUS GLYCEROL KINASE COMPLEXED WITH GLYCEROL
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: 2.75 Å
AuthorsYeh, J.I. / Charrier, V. / Paulo, J. / Hou, L. / Darbon, E. / Hol, W.G.J. / 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. / Clairborn, A. / Hol, W.G.J. / Deutscher, J.
History
DepositionOct 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)107,4624
Polymers107,2782
Non-polymers1842
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-9 kcal/mol
Surface area41680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.010, 107.670, 201.450
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: 53638.984 Da / Num. of mol.: 2
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 9

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Sample preparation

CrystalDensity Matthews: 3.44 Å3/Da / Density % sol: 64.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Sodium acetate, PEG 4000, Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 28, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 18705 / % possible obs: 92.3 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.073 / Rsym value: 0.051 / Net I/σ(I): 7.2
Reflection shellResolution: 2.75→2.87 Å / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.13 / % possible all: 87.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNS1refinement
RefinementMethod to determine structure: MIR / Resolution: 2.75→6 Å / Isotropic thermal model: ISOTROPIC / σ(F): 3 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1871 10 %RANDOM
Rwork0.242 ---
all0.26 18705 --
obs0.242 18705 87 %-
Displacement parametersBiso mean: 35.1 Å2
Refine analyzeLuzzati sigma a free: 0.1 Å
Refinement stepCycle: LAST / Resolution: 2.75→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7545 0 12 0 7557

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