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- PDB-6zq8: Crystal structure of Chaetomium thermophilum Glycerol Kinase in P... -

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Basic information

Entry
Database: PDB / ID: 6zq8
TitleCrystal structure of Chaetomium thermophilum Glycerol Kinase in P3221 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: 2.38 Å
AuthorsWilk, P. / Wator, E. / Malecki, P. / Tokarz, 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
B: Glycerol kinase-like protein
A: Glycerol kinase-like protein


Theoretical massNumber of molelcules
Total (without water)114,1352
Polymers114,1352
Non-polymers00
Water1,33374
1
A: Glycerol kinase-like protein

B: Glycerol kinase-like protein


Theoretical massNumber of molelcules
Total (without water)114,1352
Polymers114,1352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area2740 Å2
ΔGint-14 kcal/mol
Surface area39150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.145, 92.145, 232.954
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-628-

HOH

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.5 Å3/Da / Density % sol: 50.83 %
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: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.38→47.04 Å / Num. obs: 46200 / % possible obs: 98.8 % / Redundancy: 19.242 % / Biso Wilson estimate: 66.893 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.124 / Rrim(I) all: 0.127 / Χ2: 1.077 / Net I/σ(I): 17.95 / Num. measured all: 888970
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
2.38-2.5319.4121.9641.49135787742069950.6332.01794.3
2.53-2.719.3721.1842.68135954701970180.8361.216100
2.7-2.9219.9520.6465.01130150652365230.9460.663100
2.92-3.1920.2950.3549.46122540603960380.9830.363100
3.19-3.5718.930.18718.13103718547954790.9950.192100
3.57-4.1218.0980.1228.4385551486847270.9970.12497.1
4.12-5.0318.6170.07244.0177613416941690.9990.074100
5.03-7.0719.1710.0649.0563033328832880.9990.062100
7.07-47.0417.6380.03767.0534624197119630.9990.03999.6

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Processing

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

2d4w


Resolution: 2.38→47.04 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2845 2100 4.55 %
Rwork0.2438 44095 -
obs0.2456 46195 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 222.54 Å2 / Biso mean: 88.2821 Å2 / Biso min: 36.25 Å2
Refinement stepCycle: final / Resolution: 2.38→47.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7802 0 0 74 7876
Biso mean---59.42 -
Num. residues----1021
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.38-2.440.3791200.3682524264486
2.44-2.50.39241400.328429503090100
2.5-2.570.33321400.308629243064100
2.57-2.640.3711380.312129163054100
2.64-2.730.33271400.299329263066100
2.73-2.820.32171390.295629243063100
2.82-2.940.36191410.306929683109100
2.94-3.070.36141420.304729663108100
3.07-3.230.3481390.283629223061100
3.23-3.440.32361420.269729893131100
3.44-3.70.30651370.26962870300796
3.7-4.070.29281400.22942948308899
4.07-4.660.22851440.196530133157100
4.66-5.870.24281450.209830523197100
5.87-47.040.23981530.207632033356100
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)
14.1221.64350.20382.3906-0.65162.3562-0.09790.0405-1.1802-0.38440.1018-0.85160.60360.6982-00.85710.17760.18220.8118-0.00531.021970.59271.06312.0609
21.4881.6201-0.90722.5776-1.54022.3785-0.0260.34410.0007-0.51350.00970.08870.2341-0.095100.5850.1454-0.02830.5523-0.10090.445945.2628-2.024213.2321
32.8899-1.39440.06583.63720.58411.4090.30250.3255-0.3058-0.1859-0.54260.6796-0.0439-0.4062-00.5610.143-0.04130.6465-0.16560.661114.649631.349822.0654
42.2381-0.8221.20741.4243-0.26032.1890.16390.25920.4215-0.0685-0.3151-0.0478-0.27360.0652-00.48850.00790.06730.4635-0.03380.54139.090226.156929.8863
51.6464-1.79781.68020.74990.12651.70270.17590.64640.6966-0.0038-0.3737-0.4469-0.440.276500.56150.0860.22250.64940.15180.770640.280230.547224.4264
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 67 through 331 )A67 - 331
2X-RAY DIFFRACTION2chain 'A' and (resid 332 through 583 )A332 - 583
3X-RAY DIFFRACTION3chain 'B' and (resid 65 through 340 )B65 - 340
4X-RAY DIFFRACTION4chain 'B' and (resid 341 through 511 )B341 - 511
5X-RAY DIFFRACTION5chain 'B' and (resid 512 through 583 )B512 - 583

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