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- PDB-3h45: Glycerol Kinase H232E with Ethylene Glycol -

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Basic information

Entry
Database: PDB / ID: 3h45
TitleGlycerol Kinase H232E with Ethylene Glycol
ComponentsGlycerol kinase
KeywordsTRANSFERASE / ethylene glycol / kinase / ATP-binding / Glycerol metabolism / Nucleotide-binding / Phosphoprotein
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
PHOSPHATE ION / Glycerol kinase
Similarity search - Component
Biological speciesEnterococcus casseliflavus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 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 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 1.3Nov 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)224,09415
Polymers223,2144
Non-polymers88011
Water5,405300
1
X: Glycerol kinase
O: Glycerol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,1739
Polymers111,6072
Non-polymers5667
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: Glycerol kinase
D: Glycerol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,9216
Polymers111,6072
Non-polymers3144
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
X: Glycerol kinase
O: Glycerol kinase
hetero molecules

C: Glycerol kinase
D: Glycerol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,09415
Polymers223,2144
Non-polymers88011
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area11410 Å2
ΔGint-72 kcal/mol
Surface area67910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.606, 105.194, 114.305
Angle α, β, γ (deg.)90.000, 114.550, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 55803.453 Da / Num. of mol.: 4 / 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.42 Å3/Da / Density % sol: 49.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: KH2PO4, PEG 8000, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.514 Å
DetectorType: RIGAKU AFC11-KAPPA / Detector: DIFFRACTOMETER / Date: Jun 8, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.514 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 73411 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rsym value: 0.09 / Net I/σ(I): 6.5
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.368 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.005data extraction
jdtprocessdata collection
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XUP

1xup


Resolution: 2.65→12 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 3
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2887 -RANDOM
Rwork0.208 ---
all0.257 71232 --
obs0.208 68345 97.9 %-
Displacement parametersBiso max: 106.87 Å2 / Biso mean: 40.25 Å2 / Biso min: 8.47 Å2
Refinement stepCycle: LAST / Resolution: 2.65→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15482 0 50 300 15832
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.361

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