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- PDB-6zq6: Crystal structure of Chaetomium thermophilum Glycerol Kinase in c... -

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Basic information

Entry
Database: PDB / ID: 6zq6
TitleCrystal structure of Chaetomium thermophilum Glycerol Kinase in complex with glycerol in P21212 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
ACETATE ION / glycerol kinase
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 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

Downloads & links

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Assembly

Deposited unit
A: Glycerol kinase-like protein
B: Glycerol kinase-like protein
C: Glycerol kinase-like protein
D: Glycerol kinase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,78910
Polymers228,2694
Non-polymers5206
Water7,404411
1
D: Glycerol kinase-like protein
hetero molecules

A: Glycerol kinase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,4115
Polymers114,1352
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area3580 Å2
ΔGint-15 kcal/mol
Surface area37430 Å2
MethodPISA
2
C: Glycerol kinase-like protein
hetero molecules

B: Glycerol kinase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,3785
Polymers114,1352
Non-polymers2433
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3520 Å2
ΔGint-15 kcal/mol
Surface area37680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.729, 222.025, 61.331
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Glycerol kinase-like protein


Mass: 57067.277 Da / Num. of mol.: 4
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.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 2.55 Å3/Da / Density % sol: 51.69 %
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: Jan 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.3→48.6 Å / Num. obs: 103148 / % possible obs: 98.5 % / Redundancy: 3.723 % / Biso Wilson estimate: 47.097 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.177 / Rrim(I) all: 0.207 / Χ2: 1.081 / Net I/σ(I): 6.8 / Num. measured all: 383976
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
2.3-2.443.8121.5910.776253416723164060.3311.8598.1
2.44-2.613.6511.1331.075633515665154320.4651.32898.5
2.61-2.813.8350.7061.815585414696145660.6960.82299.1
2.81-3.083.770.4253.025057613560134170.8680.49598.9
3.08-3.443.6840.2225.864447512266120720.9580.25998.4
3.44-3.973.7870.11811.154076710892107640.9870.13798.8
3.97-4.863.6390.06618.1233293930691500.9960.07798.3
4.86-6.843.6090.06218.0925917732871820.9970.07298
6.84-48.63.420.03228.6114225430541590.9990.03896.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2d4w

2d4w


Resolution: 2.3→48.6 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2493 2100 2.04 %
Rwork0.2138 101019 -
obs0.2145 103119 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 810.9 Å2 / Biso mean: 57.0657 Å2 / Biso min: 22.03 Å2
Refinement stepCycle: final / Resolution: 2.3→48.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15559 0 77 411 16047
Biso mean--55.77 49.33 -
Num. residues----2038
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 (%)
2.3-2.350.38551370.34696571670897
2.35-2.410.40421380.3346636677499
2.41-2.480.33411390.31666703684299
2.48-2.550.36591400.30356702684299
2.55-2.630.35091360.29366567670398
2.63-2.730.3411400.2766722686299
2.73-2.830.32371400.27096739687999
2.83-2.960.28421400.25676724686499
2.96-3.120.2761390.23726720685999
3.12-3.320.27361390.21256661680098
3.32-3.570.23431410.19746818695999
3.57-3.930.22781410.17416748688999
3.93-4.50.17411410.14966782692398
4.5-5.670.16671430.16296895703899
5.67-48.60.22661460.20477031717797
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)
11.80820.1114-0.01880.6969-0.22990.3312-0.016-0.61730.02340.2523-0.0790.2549-0.10180.2063-0.05840.37640.05710.04030.60920.04210.423-26.404266.6978-15.9314
20.0860.17870.04320.5075-0.09780.1830.1726-0.80150.2580.14-0.191-0.3826-0.29570.14720.00820.43-0.0062-0.02690.8020.12070.5395-1.463476.8299-14.4954
30.1437-0.14450.03962.26870.0140.24540.0731-1.1035-0.2160.3069-0.301-0.02090.12980.4331-0.36840.4330.00980.04141.04250.2410.459-13.704961.9932-7.9408
41.08560.4631-0.20660.5871-0.02720.3073-0.0632-0.4647-0.34120.0147-0.1448-0.12850.0180.1792-0.05660.38510.06520.00930.5770.22140.5353-12.00562.2994-21.0221
50.01180.03360.07440.33770.58391.0961-0.040.0069-0.2862-0.3167-0.0127-0.0505-0.12920.24820.02380.27670.09860.04340.38340.09840.5038-8.840367.9705-31.863
60.33140.2668-0.02381.13910.37960.92990.0708-0.23570.2391-0.0091-0.03590.3823-0.0809-0.237100.35690.028-0.03740.43040.07970.5443-22.383294.0059-35.3247
70.45460.49140.03010.48770.07740.4488-0.0425-0.0022-0.0677-0.34540.02140.0421-0.0310.089700.43320.05830.01490.35830.07550.4175-20.147776.3432-39.34
80.1920.20850.22640.21330.22280.24140.04080.3221-0.2636-0.5621-0.2650.22450.4070.23750.00010.6994-0.00730.07520.4-0.00980.4762-24.576463.4961-42.8592
90.15540.0790.00080.3781-0.0710.0126-0.16460.07540.37760.1692-0.1258-0.05040.53850.2263-0.07380.52780.01950.08560.52570.07170.407-9.797593.8276-40.902
102.07530.1557-1.36980.8236-0.08791.9963-0.0693-0.5756-0.01860.21210.10650.0403-0.08850.3464-0.00130.33940.05310.01030.45950.06280.309116.585642.6993-20.2737
110.22620.32920.03191.37160.51430.65430.0090.1010.0432-0.18110.0680.0104-0.05870.0542-00.35110.0035-0.00960.31840.05040.361916.88127.5592-41.0919
120.6161-0.2571-0.49171.17710.16640.84-0.00530.1690.0532-0.54950.0845-0.1073-0.2220.017900.4604-0.0024-0.00740.36980.05430.367619.968334.6781-45.3112
131.0208-0.4118-0.2690.82320.08431.4213-0.00430.10950.0989-0.033-0.0294-0.0948-0.0192-0.1226-00.296-0.00770.00040.26850.00520.2982-22.936726.3789-58.1867
140.2176-0.0415-0.04911.3683-0.69090.5528-0.1526-0.1005-0.00110.18780.112-0.0248-0.0748-0.0556-00.36060.0250.0080.3339-0.03320.3263-18.975610.4201-37.0687
150.90610.04810.19130.25220.12380.59970.0738-0.04390.21040.01040.0435-0.29520.16310.44140.02180.37040.0661-0.00690.49010.02130.461937.017584.0856-45.8312
160.47130.16690.36010.50970.16890.64550.20970.25510.2831-0.2424-0.1668-0.111-0.2853-0.077600.39490.08620.02450.43330.0650.377117.389693.1922-59.8896
170.3382-0.21950.22840.56270.10780.30970.16310.60280.0853-0.2442-0.0412-0.06740.0827-0.067100.45690.07060.03760.51540.01670.39225.332481.054-61.5078
181.1539-0.30540.26310.6060.15791.13720.02760.1549-0.19070.1376-0.08660.18760.3296-0.238800.4213-0.01150.00660.34050.01990.369816.836183.012-46.6901
190.1045-0.4348-0.11521.49960.22320.3814-0.225-0.11690.0790.17870.2076-0.21630.0848-0.0323-0.00690.37130.0864-0.04410.3617-0.00890.359519.8634107.5018-31.8233
200.05810.01940.09660.1632-0.06410.2084-0.3025-0.3609-0.08830.10830.4493-0.0690.10510.307600.5380.0826-0.03210.4435-0.00030.375724.596289.4042-29.555
210.5564-0.29130.00080.6495-0.00020.33-0.3523-0.4281-0.07830.96420.2314-0.05490.48050.02610.02950.7010.1140.09290.51290.13170.418423.213482.1805-25.011
220.1645-0.08030.03890.6201-0.09790.6173-0.2045-0.20220.1849-0.47080.27170.39720.4483-0.60590.02360.47820.0602-0.00260.43410.01290.45158.5897112.1122-32.144
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 65 through 173 )A65 - 173
2X-RAY DIFFRACTION2chain 'A' and (resid 174 through 212 )A174 - 212
3X-RAY DIFFRACTION3chain 'A' and (resid 213 through 258 )A213 - 258
4X-RAY DIFFRACTION4chain 'A' and (resid 259 through 340 )A259 - 340
5X-RAY DIFFRACTION5chain 'A' and (resid 341 through 383 )A341 - 383
6X-RAY DIFFRACTION6chain 'A' and (resid 384 through 446 )A384 - 446
7X-RAY DIFFRACTION7chain 'A' and (resid 447 through 525 )A447 - 525
8X-RAY DIFFRACTION8chain 'A' and (resid 526 through 559 )A526 - 559
9X-RAY DIFFRACTION9chain 'A' and (resid 560 through 583 )A560 - 583
10X-RAY DIFFRACTION10chain 'B' and (resid 64 through 340 )B64 - 340
11X-RAY DIFFRACTION11chain 'B' and (resid 341 through 489 )B341 - 489
12X-RAY DIFFRACTION12chain 'B' and (resid 490 through 583 )B490 - 583
13X-RAY DIFFRACTION13chain 'C' and (resid 64 through 383 )C64 - 383
14X-RAY DIFFRACTION14chain 'C' and (resid 384 through 583 )C384 - 583
15X-RAY DIFFRACTION15chain 'D' and (resid 64 through 146 )D64 - 146
16X-RAY DIFFRACTION16chain 'D' and (resid 147 through 212 )D147 - 212
17X-RAY DIFFRACTION17chain 'D' and (resid 213 through 258 )D213 - 258
18X-RAY DIFFRACTION18chain 'D' and (resid 259 through 383 )D259 - 383
19X-RAY DIFFRACTION19chain 'D' and (resid 384 through 489 )D384 - 489
20X-RAY DIFFRACTION20chain 'D' and (resid 490 through 525 )D490 - 525
21X-RAY DIFFRACTION21chain 'D' and (resid 526 through 559 )D526 - 559
22X-RAY DIFFRACTION22chain 'D' and (resid 560 through 583 )D560 - 583

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