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- PDB-6zq7: Crystal structure of Chaetomium thermophilum Glycerol Kinase in I... -

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Basic information

Entry
Database: PDB / ID: 6zq7
TitleCrystal structure of Chaetomium thermophilum Glycerol Kinase in I222 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 / Resolution: 2.421 Å
AuthorsWilk, P. / Wator, E. / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2213
Polymers57,0671
Non-polymers1542
Water1,31573
1
A: Glycerol kinase-like protein
hetero molecules

A: Glycerol kinase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,4436
Polymers114,1352
Non-polymers3084
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3940 Å2
ΔGint-8 kcal/mol
Surface area37740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.600, 89.437, 131.285
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Glycerol kinase-like protein


Mass: 57067.277 Da / Num. of mol.: 1
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.28 Å3/Da / Density % sol: 46.02 %
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: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.42→45.432 Å / Num. obs: 38252 / % possible obs: 99.5 % / Redundancy: 7.012 % / Biso Wilson estimate: 78.294 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.086 / Χ2: 0.747 / Net I/σ(I): 12.02 / Num. measured all: 268223
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
2.42-2.577.1071.331.1243133620060690.7241.43497.9
2.57-2.747.2810.7282.2142551584758440.8930.78499.9
2.74-2.967.0830.4643.6338355542154150.950.50199.9
2.96-3.246.7660.2366.933814500749980.9880.25599.8
3.24-3.627.280.11514.1132934452645240.9970.124100
3.62-4.186.8850.07721.8827415398939820.9980.08499.8
4.18-5.116.5320.06128.6521817335433400.9970.06699.6
5.11-7.187.0450.05732.0618339260626030.9980.06199.9
7.18-45.4326.6790.04137.739865149114770.9990.04499.1

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.16refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2d4w

2d4w


Resolution: 2.421→45.432 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2513 1008 5.01 %
Rwork0.1864 19124 -
obs0.1897 20132 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 206.71 Å2 / Biso mean: 92.8533 Å2 / Biso min: 42.01 Å2
Refinement stepCycle: final / Resolution: 2.421→45.432 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3888 0 10 73 3971
Biso mean--78.53 83.77 -
Num. residues----509
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.421-2.54860.34821390.3128263598
2.5486-2.70820.391420.26922697100
2.7082-2.91730.31631430.23892726100
2.9173-3.21080.26741430.19822707100
3.2108-3.67520.26221450.18592737100
3.6752-4.62970.22281440.16452743100
4.6297-45.4320.23351520.17322879100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.05570.1510.03121.30960.1208-0.1045-0.060.3454-0.3261-0.11270.293-0.4072-0.01630.06620.00270.4847-0.04150.05170.6303-0.11820.70427.14711.204917.486
21.6260.5740.32672.17360.25860.5018-0.41220.22310.1295-0.12030.41120.0956-0.49930.31130.01270.7493-0.2053-0.0480.65930.02060.593930.911428.265318.2241
31.2680.63510.45470.5490.67880.0105-0.1140.1076-0.1228-0.12960.2603-0.0644-0.07590.13860.0030.5443-0.10720.00690.576-0.0530.52218.73944.861615.1069
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 490 through 582 )A490 - 582
2X-RAY DIFFRACTION2chain 'A' and (resid 65 through 337 )A65 - 337
3X-RAY DIFFRACTION3chain 'A' and (resid 338 through 489 )A338 - 489

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