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- PDB-1pie: Crystal Structure of Lactococcus lactis Galactokinase Complexed w... -

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Basic information

Entry
Database: PDB / ID: 1pie
TitleCrystal Structure of Lactococcus lactis Galactokinase Complexed with Galactose
ComponentsGalactokinase
KeywordsTRANSFERASE / galactose / galactosemia / kinase
Function / homology
Function and homology information


galactokinase / galactokinase activity / galactose metabolic process / magnesium ion binding / ATP binding / cytosol
Similarity search - Function
Galactokinase, bacterial / Galactokinase, N-terminal domain / Galactokinase, conserved site / Galactokinase galactose-binding signature / Galactokinase signature. / Galactokinase / Mevalonate/galactokinase / GHMP kinase, ATP-binding, conserved site / GHMP kinases putative ATP-binding domain. / GHMP kinase, C-terminal domain ...Galactokinase, bacterial / Galactokinase, N-terminal domain / Galactokinase, conserved site / Galactokinase galactose-binding signature / Galactokinase signature. / Galactokinase / Mevalonate/galactokinase / GHMP kinase, ATP-binding, conserved site / GHMP kinases putative ATP-binding domain. / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase, C-terminal domain / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-D-galactopyranose / PHOSPHATE ION / Galactokinase
Similarity search - Component
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsThoden, J.B. / Holden, H.M.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Molecular Structure of Galactokinase
Authors: Thoden, J.B. / Holden, H.M.
History
DepositionMay 30, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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
A: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3603
Polymers46,0851
Non-polymers2752
Water2,954164
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.400, 143.400, 143.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Galactokinase / Galactose kinase


Mass: 46084.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Gene: GALK / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q9R7D7, galactokinase
#2: Sugar ChemComp-GLA / alpha-D-galactopyranose / alpha-D-galactose / D-galactose / galactose / ALPHA D-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.67 Å3/Da / Density % sol: 53.86 %
Crystal growTemperature: 277 K / Method: batch / pH: 9
Details: sodium phosphate, potassium phosphate, CHES, galactose, pH 9, batch, temperature 277K
Crystal grow
*PLUS
pH: 7.5 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMHEPES11pH7.5
2200 mM11NaCl
315 mg/mlprotein12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97932, 0.97951, 0.96411, 0.65255
DetectorType: SBC-2 / Detector: CCD / Date: Apr 4, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979321
20.979511
30.964111
40.652551
ReflectionResolution: 2.1→20 Å / Num. all: 28616 / Num. obs: 28616 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14 % / Rsym value: 0.067 / Net I/σ(I): 75.4
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 9.7 % / Mean I/σ(I) obs: 9.3 / Num. unique all: 2804 / Rsym value: 0.214 / % possible all: 99.5
Reflection
*PLUS
Rmerge(I) obs: 0.067
Reflection shell
*PLUS
% possible obs: 99.5 % / Num. unique obs: 2804 / Rmerge(I) obs: 0.214

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Processing

Software
NameClassification
d*TREKdata scaling
HKL-2000data reduction
SOLVEphasing
TNTrefinement
d*TREKdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.266 2896 -random
Rwork0.199 ---
all0.204 28536 --
obs0.204 28536 98.7 %-
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2985 0 17 164 3166
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.013
X-RAY DIFFRACTIONt_angle_deg2.59
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg18.1
X-RAY DIFFRACTIONt_planar_d0.006
X-RAY DIFFRACTIONt_plane_restr0.012

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