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- PDB-6zq5: Crystal structure of Chaetomium thermophilum Glycerol Kinase in P... -

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Basic information

Entry
Database: PDB / ID: 6zq5
TitleCrystal structure of Chaetomium thermophilum Glycerol Kinase in P2221 space group
ComponentsGlycerol kinase-like protein
KeywordsTRANSFERASE / Kinase / Glycerol / Metabolism
Function / homology
Function and homology information


glycerol-3-phosphate biosynthetic process / glycerol kinase / glycerol kinase activity / glycerol catabolic process / triglyceride metabolic process / mitochondrion / ATP binding
Similarity search - Function
Glycerol kinase, metazoa / 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 ...Glycerol kinase, metazoa / 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 speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.14 Å
AuthorsWilk, P. / Wator, E. / Malecki, P. / Grudnik, P.
Funding support Poland, 2items
OrganizationGrant numberCountry
Polish National Science CentreUMO-2015/19/D/NZ1/02009 Poland
Foundation for Polish ScienceTEAM TECH CORE FACILITY/2017-4/6 Poland
CitationJournal: Int J Mol Sci / Year: 2020
Title: Structural Characterization of Glycerol Kinase from the Thermophilic Fungus Chaetomium thermophilum .
Authors: Wilk, P. / Kuska, K. / Wator, E. / Malecki, P.H. / Wos, K. / Tokarz, P. / Dubin, G. / Grudnik, P.
History
DepositionJul 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Glycerol kinase-like protein
B: Glycerol kinase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,63110
Polymers114,1352
Non-polymers4978
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint27 kcal/mol
Surface area40050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.565, 111.468, 171.252
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221

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Components

#1: Protein Glycerol kinase-like protein


Mass: 57067.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Gene: CTHT_0042250 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SAG9
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.66 Å3/Da / Density % sol: 53.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.125-0.3 M CaCl2; 16-19% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.14→46.71 Å / Num. obs: 61278 / % possible obs: 89.9 % / Redundancy: 6.118 % / Biso Wilson estimate: 47.968 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.119 / Rrim(I) all: 0.13 / Χ2: 1.059 / Net I/σ(I): 11.59 / Num. measured all: 374918
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.14-2.274.722.1970.67381781086780880.2762.43574.4
2.27-2.425.2671.3121.21421261021979980.4941.44378.3
2.42-2.625.4960.8322.0245102953182070.7350.91286.1
2.62-2.875.760.4413.9348086881783480.8990.48494.7
2.87-3.27.0280.2467.8956010800479690.9740.26599.6
3.2-3.76.9970.11616.1749499709670740.9930.12699.7
3.7-4.527.3420.0629.7444390605060460.9980.06499.9
4.52-6.366.90.04634.1732801477747540.9980.0599.5
6.36-46.716.7020.03145.2318726282127940.9990.03499

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2d4w

2d4w


Resolution: 2.14→46.71 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2495 --
Rwork0.2155 --
obs-61158 89.9 %
Displacement parametersBiso max: 135.37 Å2 / Biso mean: 58.8501 Å2 / Biso min: 24.94 Å2
Refinement stepCycle: LAST / Resolution: 2.14→46.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7796 0 32 318 8146

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