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- PDB-6k79: Glycerol kinase form Thermococcus kodakarensis, complex structure... -

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Basic information

Entry
Database: PDB / ID: 6k79
TitleGlycerol kinase form Thermococcus kodakarensis, complex structure with substrate.
Components(Glycerol kinase) x 2
KeywordsTRANSFERASE / Glycerol / Kinase / ATP / Archaea
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 / 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
TRIETHYLENE GLYCOL / Glycerol kinase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsKoga, Y. / Angkawidjaja, C. / Matsumura, H. / Hokao, R.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP22780091 Japan
CitationJournal: To Be Published
Title: Structural analysis of hexameric structure of glycerol kinase from Thermococcus kodakaraeinsis KOD1
Authors: Hokao, R. / Matsumura, H. / Katsumi, R. / Angkawidjaja, C. / Takano, K. / Kanaya, S. / Koga, Y.
History
DepositionJun 6, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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

Downloads & links

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Assembly

Deposited unit
B: Glycerol kinase
C: Glycerol kinase
D: Glycerol kinase
A: Glycerol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,86212
Polymers223,8934
Non-polymers9698
Water8,233457
1
A: Glycerol kinase
hetero molecules

B: Glycerol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,4386
Polymers111,9542
Non-polymers4854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_645x+1,y-1,z1
Buried area4280 Å2
ΔGint-10 kcal/mol
Surface area36940 Å2
MethodPISA
2
C: Glycerol kinase
hetero molecules

D: Glycerol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,4236
Polymers111,9392
Non-polymers4854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_644x+1,y-1,z-11
Buried area4330 Å2
ΔGint-7 kcal/mol
Surface area37210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.041, 72.128, 115.994
Angle α, β, γ (deg.)103.43, 94.96, 99.48
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 55984.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: glpK, TK1396 / Production host: Escherichia coli (E. coli) / References: UniProt: O93623, glycerol kinase
#2: Protein Glycerol kinase / / ATP:glycerol 3-phosphotransferase / Glycerokinase / GK


Mass: 55969.410 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: glpK, TK1396 / Production host: Escherichia coli (E. coli) / References: UniProt: O93623, glycerol kinase
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 457 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.38 Å3/Da / Density % sol: 48.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: Imidazole, PEG1000, Calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: AGILENT EOS CCD / Detector: CCD / Date: Nov 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 109477 / % possible obs: 98.6 % / Redundancy: 4 % / Net I/σ(I): 14.42
Reflection shellResolution: 2.15→2.19 Å / Num. unique obs: 5423

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→46.2 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.661 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.214 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23776 5226 5 %RANDOM
Rwork0.1846 ---
obs0.18724 99716 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.575 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20.01 Å2
2--0 Å2-0.01 Å2
3---0.05 Å2
Refinement stepCycle: 1 / Resolution: 2.19→46.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15585 0 64 457 16106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01515969
X-RAY DIFFRACTIONr_bond_other_d0.0010.01714581
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.73221607
X-RAY DIFFRACTIONr_angle_other_deg0.4961.70734062
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.60151957
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.92218.05559
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.872152282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.53615112
X-RAY DIFFRACTIONr_chiral_restr0.0630.22069
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217935
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023019
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.373.1627840
X-RAY DIFFRACTIONr_mcbond_other2.373.1627841
X-RAY DIFFRACTIONr_mcangle_it3.5534.7359793
X-RAY DIFFRACTIONr_mcangle_other3.5524.7359794
X-RAY DIFFRACTIONr_scbond_it3.2893.6468129
X-RAY DIFFRACTIONr_scbond_other3.2893.6468129
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1755.28611815
X-RAY DIFFRACTIONr_long_range_B_refined6.55338.8617698
X-RAY DIFFRACTIONr_long_range_B_other6.55338.86117699
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.19→2.247 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 381 -
Rwork0.258 7350 -
obs--97.82 %

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