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

ID or keywords:

Entry

Database: PDB / ID: 6zq6

Title

Crystal structure of Chaetomium thermophilum Glycerol Kinase in complex with glycerol in P21212 space group

Components

Glycerol kinase-like protein

Keywords

TRANSFERASE / Kinase / Glycerol / Metabolism

Function / homology

Function and homology information

glycerol-3-phosphate metabolic process / glycerol kinase / glycerol kinase activity / glycerol catabolic process / ATP binding
Similarity search - Function

Biological species

Chaetomium thermophilum (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.3 Å

Authors

Wilk, P. / Wator, E. / Grudnik, P.

Funding support

Poland, 2items

Citation

Journal: 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

Deposition	Jul 9, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 23, 2020	Provider: repository / Type: Initial release
Revision 1.1	Dec 30, 2020	Group: 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 1.2	Jan 31, 2024	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6zq6.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb6zq6.ent.gz	947.5 KB	Display	PDB format
PDBx/mmJSON format	6zq6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6zq6_validation.pdf.gz	481.1 KB	Display	wwPDB validaton report
Full document	6zq6_full_validation.pdf.gz	496.3 KB	Display
Data in XML	6zq6_validation.xml.gz	72.3 KB	Display
Data in CIF	6zq6_validation.cif.gz	99.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zq/6zq6 ftp://data.pdbj.org/pub/pdb/validation_reports/zq/6zq6	HTTPS FTP

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Related structure data

Related structure data	6zq4C 6zq5C 6zq7C 6zq8C 2d4wS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6jae-2 6zq8-1 2d4w-d 6jaf-d 3wxk-2 5azj-2 5azj-1 6k79-1 6j9q-2 5gn6-2 6k79-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Glycerol kinase-like protein

B: Glycerol kinase-like protein

C: Glycerol kinase-like protein

D: Glycerol kinase-like protein

hetero molecules

229 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

D: Glycerol kinase-like protein

hetero molecules

A: Glycerol kinase-like protein

hetero molecules

defined by author&software
Evidence: light scattering, MALS
114 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Glycerol kinase-like protein

hetero molecules

B: Glycerol kinase-like protein

hetero molecules

defined by author&software
114 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	18
Space group name H-M	P2₁2₁2

#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 interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.55 Å³/Da / Density % sol: 51.69 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.125-0.3 M CaCl2; 16-19% PEG 3350

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

BESSY

/ Beamline: 14.1 / Wavelength: 0.9184 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 29, 2019

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9184 Å / Relative weight: 1

Reflection

Resolution: 2.3→48.6 Å / Num. obs: 103148 / % possible obs: 98.5 % / Redundancy: 3.723 % / B_iso Wilson estimate: 47.097 Å² / CC_1/2: 0.993 / R_merge(I) obs: 0.177 / R_rim(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 (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.3-2.44	3.812	1.591	0.77	62534	16723	16406	0.331	1.85	98.1
2.44-2.61	3.651	1.133	1.07	56335	15665	15432	0.465	1.328	98.5
2.61-2.81	3.835	0.706	1.81	55854	14696	14566	0.696	0.822	99.1
2.81-3.08	3.77	0.425	3.02	50576	13560	13417	0.868	0.495	98.9
3.08-3.44	3.684	0.222	5.86	44475	12266	12072	0.958	0.259	98.4
3.44-3.97	3.787	0.118	11.15	40767	10892	10764	0.987	0.137	98.8
3.97-4.86	3.639	0.066	18.12	33293	9306	9150	0.996	0.077	98.3
4.86-6.84	3.609	0.062	18.09	25917	7328	7182	0.997	0.072	98
6.84-48.6	3.42	0.032	28.61	14225	4305	4159	0.999	0.038	96.6

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
XSCALE		data scaling
PHASER		phasing
PDB_EXTRACT	3.25	data extraction
XDS		data reduction

Refinement

Method 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

	R_factor	Num. reflection	% reflection
R_free	0.2493	2100	2.04 %
R_work	0.2138	101019	-
obs	0.2145	103119	98.47 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 810.9 Å² / B_iso mean: 57.0657 Å² / B_iso min: 22.03 Å²

Refinement step

Cycle: final / Resolution: 2.3→48.6 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15559	0	77	411	16047
B_iso mean	-	-	55.77	49.33	-
Num. residues	-	-	-	-	2038

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.3-2.35	0.3855	137	0.3469	6571	6708	97
2.35-2.41	0.4042	138	0.334	6636	6774	99
2.41-2.48	0.3341	139	0.3166	6703	6842	99
2.48-2.55	0.3659	140	0.3035	6702	6842	99
2.55-2.63	0.3509	136	0.2936	6567	6703	98
2.63-2.73	0.341	140	0.276	6722	6862	99
2.73-2.83	0.3237	140	0.2709	6739	6879	99
2.83-2.96	0.2842	140	0.2567	6724	6864	99
2.96-3.12	0.276	139	0.2372	6720	6859	99
3.12-3.32	0.2736	139	0.2125	6661	6800	98
3.32-3.57	0.2343	141	0.1974	6818	6959	99
3.57-3.93	0.2278	141	0.1741	6748	6889	99
3.93-4.5	0.1741	141	0.1496	6782	6923	98
4.5-5.67	0.1667	143	0.1629	6895	7038	99
5.67-48.6	0.2266	146	0.2047	7031	7177	97

Refinement TLS params.

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

ID	L11 (°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)
1	1.8082	0.1114	-0.0188	0.6969	-0.2299	0.3312	-0.016	-0.6173	0.0234	0.2523	-0.079	0.2549	-0.1018	0.2063	-0.0584	0.3764	0.0571	0.0403	0.6092	0.0421	0.423	-26.4042	66.6978	-15.9314
2	0.086	0.1787	0.0432	0.5075	-0.0978	0.183	0.1726	-0.8015	0.258	0.14	-0.191	-0.3826	-0.2957	0.1472	0.0082	0.43	-0.0062	-0.0269	0.802	0.1207	0.5395	-1.4634	76.8299	-14.4954
3	0.1437	-0.1445	0.0396	2.2687	0.014	0.2454	0.0731	-1.1035	-0.216	0.3069	-0.301	-0.0209	0.1298	0.4331	-0.3684	0.433	0.0098	0.0414	1.0425	0.241	0.459	-13.7049	61.9932	-7.9408
4	1.0856	0.4631	-0.2066	0.5871	-0.0272	0.3073	-0.0632	-0.4647	-0.3412	0.0147	-0.1448	-0.1285	0.018	0.1792	-0.0566	0.3851	0.0652	0.0093	0.577	0.2214	0.5353	-12.005	62.2994	-21.0221
5	0.0118	0.0336	0.0744	0.3377	0.5839	1.0961	-0.04	0.0069	-0.2862	-0.3167	-0.0127	-0.0505	-0.1292	0.2482	0.0238	0.2767	0.0986	0.0434	0.3834	0.0984	0.5038	-8.8403	67.9705	-31.863
6	0.3314	0.2668	-0.0238	1.1391	0.3796	0.9299	0.0708	-0.2357	0.2391	-0.0091	-0.0359	0.3823	-0.0809	-0.2371	0	0.3569	0.028	-0.0374	0.4304	0.0797	0.5443	-22.3832	94.0059	-35.3247
7	0.4546	0.4914	0.0301	0.4877	0.0774	0.4488	-0.0425	-0.0022	-0.0677	-0.3454	0.0214	0.0421	-0.031	0.0897	0	0.4332	0.0583	0.0149	0.3583	0.0755	0.4175	-20.1477	76.3432	-39.34
8	0.192	0.2085	0.2264	0.2133	0.2228	0.2414	0.0408	0.3221	-0.2636	-0.5621	-0.265	0.2245	0.407	0.2375	0.0001	0.6994	-0.0073	0.0752	0.4	-0.0098	0.4762	-24.5764	63.4961	-42.8592
9	0.1554	0.079	0.0008	0.3781	-0.071	0.0126	-0.1646	0.0754	0.3776	0.1692	-0.1258	-0.0504	0.5385	0.2263	-0.0738	0.5278	0.0195	0.0856	0.5257	0.0717	0.407	-9.7975	93.8276	-40.902
10	2.0753	0.1557	-1.3698	0.8236	-0.0879	1.9963	-0.0693	-0.5756	-0.0186	0.2121	0.1065	0.0403	-0.0885	0.3464	-0.0013	0.3394	0.0531	0.0103	0.4595	0.0628	0.3091	16.5856	42.6993	-20.2737
11	0.2262	0.3292	0.0319	1.3716	0.5143	0.6543	0.009	0.101	0.0432	-0.1811	0.068	0.0104	-0.0587	0.0542	-0	0.3511	0.0035	-0.0096	0.3184	0.0504	0.3619	16.881	27.5592	-41.0919
12	0.6161	-0.2571	-0.4917	1.1771	0.1664	0.84	-0.0053	0.169	0.0532	-0.5495	0.0845	-0.1073	-0.222	0.0179	0	0.4604	-0.0024	-0.0074	0.3698	0.0543	0.3676	19.9683	34.6781	-45.3112
13	1.0208	-0.4118	-0.269	0.8232	0.0843	1.4213	-0.0043	0.1095	0.0989	-0.033	-0.0294	-0.0948	-0.0192	-0.1226	-0	0.296	-0.0077	0.0004	0.2685	0.0052	0.2982	-22.9367	26.3789	-58.1867
14	0.2176	-0.0415	-0.0491	1.3683	-0.6909	0.5528	-0.1526	-0.1005	-0.0011	0.1878	0.112	-0.0248	-0.0748	-0.0556	-0	0.3606	0.025	0.008	0.3339	-0.0332	0.3263	-18.9756	10.4201	-37.0687
15	0.9061	0.0481	0.1913	0.2522	0.1238	0.5997	0.0738	-0.0439	0.2104	0.0104	0.0435	-0.2952	0.1631	0.4414	0.0218	0.3704	0.0661	-0.0069	0.4901	0.0213	0.4619	37.0175	84.0856	-45.8312
16	0.4713	0.1669	0.3601	0.5097	0.1689	0.6455	0.2097	0.2551	0.2831	-0.2424	-0.1668	-0.111	-0.2853	-0.0776	0	0.3949	0.0862	0.0245	0.4333	0.065	0.3771	17.3896	93.1922	-59.8896
17	0.3382	-0.2195	0.2284	0.5627	0.1078	0.3097	0.1631	0.6028	0.0853	-0.2442	-0.0412	-0.0674	0.0827	-0.0671	0	0.4569	0.0706	0.0376	0.5154	0.0167	0.392	25.3324	81.054	-61.5078
18	1.1539	-0.3054	0.2631	0.606	0.1579	1.1372	0.0276	0.1549	-0.1907	0.1376	-0.0866	0.1876	0.3296	-0.2388	0	0.4213	-0.0115	0.0066	0.3405	0.0199	0.3698	16.8361	83.012	-46.6901
19	0.1045	-0.4348	-0.1152	1.4996	0.2232	0.3814	-0.225	-0.1169	0.079	0.1787	0.2076	-0.2163	0.0848	-0.0323	-0.0069	0.3713	0.0864	-0.0441	0.3617	-0.0089	0.3595	19.8634	107.5018	-31.8233
20	0.0581	0.0194	0.0966	0.1632	-0.0641	0.2084	-0.3025	-0.3609	-0.0883	0.1083	0.4493	-0.069	0.1051	0.3076	0	0.538	0.0826	-0.0321	0.4435	-0.0003	0.3757	24.5962	89.4042	-29.555
21	0.5564	-0.2913	0.0008	0.6495	-0.0002	0.33	-0.3523	-0.4281	-0.0783	0.9642	0.2314	-0.0549	0.4805	0.0261	0.0295	0.701	0.114	0.0929	0.5129	0.1317	0.4184	23.2134	82.1805	-25.011
22	0.1645	-0.0803	0.0389	0.6201	-0.0979	0.6173	-0.2045	-0.2022	0.1849	-0.4708	0.2717	0.3972	0.4483	-0.6059	0.0236	0.4782	0.0602	-0.0026	0.4341	0.0129	0.4515	8.5897	112.1122	-32.144

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 65 through 173 )	A	65 - 173
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 174 through 212 )	A	174 - 212
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 213 through 258 )	A	213 - 258
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 259 through 340 )	A	259 - 340
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 341 through 383 )	A	341 - 383
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 384 through 446 )	A	384 - 446
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 447 through 525 )	A	447 - 525
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 526 through 559 )	A	526 - 559
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 560 through 583 )	A	560 - 583
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 64 through 340 )	B	64 - 340
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 341 through 489 )	B	341 - 489
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 490 through 583 )	B	490 - 583
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 64 through 383 )	C	64 - 383
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 384 through 583 )	C	384 - 583
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 64 through 146 )	D	64 - 146
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 147 through 212 )	D	147 - 212
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 213 through 258 )	D	213 - 258
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 259 through 383 )	D	259 - 383
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 384 through 489 )	D	384 - 489
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 490 through 525 )	D	490 - 525
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 526 through 559 )	D	526 - 559
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 560 through 583 )	D	560 - 583

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