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- PDB-6k76: Glycerol kinase form Thermococcus kodakarensis, complex structure... -

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Basic information

Entry
Database: PDB / ID: 6k76
TitleGlycerol kinase form Thermococcus kodakarensis, complex structure with substrate.
ComponentsGlycerol kinase
KeywordsTRANSFERASE / Glycerol / Kinase / ATP / Archaea
Function / homology
Function and homology information


glycerol-3-phosphate metabolic process / glycerol kinase / glycerol kinase activity / glycerol metabolic process / glycerol catabolic process / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Glycerol kinase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 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
A: Glycerol kinase
B: Glycerol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,9514
Polymers111,9392
Non-polymers1,0122
Water00
1
A: Glycerol kinase
hetero molecules

B: Glycerol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,9514
Polymers111,9392
Non-polymers1,0122
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area4470 Å2
ΔGint-19 kcal/mol
Surface area35690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.862, 218.862, 66.244
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 55969.477 Da / Num. of mol.: 2
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: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
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: 2.8 Å3/Da / Density % sol: 56.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: imidazole, PEG1000, Calcium acetate, glycerol, AMP-PCP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Jul 20, 2009
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.049→50 Å / Num. obs: 22560 / % possible obs: 99.9 % / Redundancy: 5.8 % / Net I/σ(I): 23.49
Reflection shellResolution: 3.05→3.16 Å / Num. unique obs: 2237

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Processing

Software
NameVersionClassification
PHENIX(dev_3071: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→41.361 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.93
RfactorNum. reflection% reflectionSelection details
Rfree0.2606 1151 5.11 %random
Rwork0.1847 ---
obs0.1886 22523 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.05→41.361 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7674 0 62 0 7736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117894
X-RAY DIFFRACTIONf_angle_d1.26710701
X-RAY DIFFRACTIONf_dihedral_angle_d8.7994680
X-RAY DIFFRACTIONf_chiral_restr0.0681186
X-RAY DIFFRACTIONf_plane_restr0.0061358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0491-3.18780.31071600.24122640X-RAY DIFFRACTION100
3.1878-3.35580.30921350.22972697X-RAY DIFFRACTION100
3.3558-3.5660.2961460.21682679X-RAY DIFFRACTION100
3.566-3.84110.28871520.20352640X-RAY DIFFRACTION100
3.8411-4.22730.25831450.18662675X-RAY DIFFRACTION100
4.2273-4.83820.24781210.16312694X-RAY DIFFRACTION100
4.8382-6.09250.24381540.17642683X-RAY DIFFRACTION100
6.0925-41.36480.23141380.16212664X-RAY DIFFRACTION100

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