PDB-3rf6: Crystal structure of glycerol-3 phosphate bound HAD-like phosphat...

ID or keywords:

Entry

Database: PDB / ID: 3rf6

Title

Crystal structure of glycerol-3 phosphate bound HAD-like phosphatase from Saccharomyces cerevisiae

Components

Uncharacterized protein YKR070W

Keywords

HYDROLASE / PSI-2 / MCSG / Structural Genomics / Midwest Center for Structural Genomics / haloacid dehalogenase-like hydrolase / mitochondria / phosphatase

Function / homology

Function and homology information

glycerophospholipid biosynthetic process / Hydrolases / hydrolase activity / mitochondrion
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / 3KC2 / Resolution: 1.695 Å

Authors

Nocek, B. / Kuznetsova, K. / Evdokimova, E. / Savchenko, A. / Iakunine, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: TO BE PUBLISHED
Title: Crystal structure of glycerol-3 phosphate bound HAD-like phosphatase from Saccharomyces cerevisiae
Authors: Nocek, B. / Kuznetsova, K. / Evdokimova, E. / Savchenko, A. / Iakunine, A. / Joachimiak, A.

History

Deposition	Apr 5, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 1, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Jan 24, 2018	Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3	Feb 7, 2018	Group: Structure summary / Category: audit_author
Revision 1.4	Feb 21, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3rf6.cif.gz	296.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3rf6.ent.gz	239.8 KB	Display	PDB format
PDBx/mmJSON format	3rf6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3rf6_validation.pdf.gz	478 KB	Display	wwPDB validaton report
Full document	3rf6_full_validation.pdf.gz	483.4 KB	Display
Data in XML	3rf6_validation.xml.gz	32.1 KB	Display
Data in CIF	3rf6_validation.cif.gz	48.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rf/3rf6 ftp://data.pdbj.org/pub/pdb/validation_reports/rf/3rf6	HTTPS FTP

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Related structure data

Related structure data	3kc2
Similar structure data	4r5m-d 2h6e-2 6t8y-2 5urb-1 5urb-2 4lmq-1 6t8y-1 5bnt-2 4ffz-2 4r6u-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: apc7327

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1) #215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1)

Deposited unit

A: Uncharacterized protein YKR070W

B: Uncharacterized protein YKR070W

hetero molecules

80.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

2

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	59.912, 71.652, 195.428
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Uncharacterized protein YKR070W Mass: 39683.137 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: YKR070W / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: P36151
#2: Chemical	ChemComp-FLC / CITRATE ANION Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₅O₇
#3: Chemical	ChemComp-G3P / SN-GLYCEROL-3-PHOSPHATE Mass: 172.074 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₉O₆P
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 545 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.64 Å³/Da / Density % sol: 53.45 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 200mM NA citrate, HEPES, 2mM MGCL2, PH 7.5, 30mM glycerol-3-phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 27, 2010 / Details: mirrors
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 1.7→40 Å / Num. all: 94039 / Num. obs: 93836 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6 % / B_iso Wilson estimate: 24.79 Å² / R_merge(I) obs: 0.07 / Net I/σ(I): 30
Reflection shell	Resolution: 1.7→1.73 Å / % possible all: 100

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
MOLREP		phasing
PHENIX	(phenix.refine: 1.6.4_486)	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure: 3KC2 / Resolution: 1.695→35.239 Å / SU ML: 0.21 / σ(F): 1.33 / σ(I): 0 / Phase error: 19.47 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1935	4701	5.02 %	Random
R_work	0.1642	-	-	-
all	0.17	98422	-	-
obs	0.1657	93721	99.44 %	-

Solvent computation

Shrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 44.177 Å² / k_sol: 0.406 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	7.2836 Å²	-0 Å²	-0 Å²
2-	-	-6.0848 Å²	0 Å²
3-	-	-	-1.1988 Å²

Refinement step

Cycle: LAST / Resolution: 1.695→35.239 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5394	0	49	545	5988

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.021	5613
X-RAY DIFFRACTION	f_angle_d	1.533	7655
X-RAY DIFFRACTION	f_dihedral_angle_d	13.511	2072
X-RAY DIFFRACTION	f_chiral_restr	0.111	848
X-RAY DIFFRACTION	f_plane_restr	0.009	990

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.695-1.7556	0.307	473	0.2769	8523	X-RAY DIFFRACTION	97
1.7556-1.8259	0.3013	441	0.2454	8881	X-RAY DIFFRACTION	100
1.8259-1.909	0.2306	482	0.1985	8810	X-RAY DIFFRACTION	100
1.909-2.0096	0.2263	445	0.1747	8863	X-RAY DIFFRACTION	100
2.0096-2.1355	0.1839	436	0.1556	8933	X-RAY DIFFRACTION	100
2.1355-2.3004	0.1855	454	0.1465	8925	X-RAY DIFFRACTION	100
2.3004-2.5318	0.1843	476	0.1546	8920	X-RAY DIFFRACTION	100
2.5318-2.898	0.2146	463	0.1724	8985	X-RAY DIFFRACTION	100
2.898-3.6506	0.2019	508	0.1666	9017	X-RAY DIFFRACTION	100
3.6506-35.2464	0.159	523	0.1457	9163	X-RAY DIFFRACTION	98

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	0.5318	-0.1224	0.0904	0.5464	-0.0937	0.1657	-0.1596	-0.4752	0.0301	0.5965	0.2551	-0.0256	-0.1198	0.0371	-0.0928	0.5536	0.078	0.0244	0.3842	0.0255	0.1822	-17.8766	-5.4938	38.5578
2	1.4513	-0.2263	-0.0275	0.7751	0.0219	0.0828	-0.0674	-0.6149	-0.1274	0.6946	0.2786	0.0206	-0.1841	-0.0661	-0.1887	0.4973	0.0948	0.0443	0.3766	0.0923	0.2095	-24.0498	-10.8157	35.4881
3	0.3508	-0.0664	-0.2941	1.3308	0.5656	0.4534	-0.087	-0.3904	-0.3798	0.5546	0.0942	0.2941	-0.0065	0.0001	0.0785	0.3993	0.0518	0.1018	0.3855	0.1265	0.2819	-26.4508	-11.2503	33.5193
4	1.7326	-1.4655	-1.3924	3.1869	-0.3605	3.6598	-0.0361	0.1245	-0.3485	0.4026	0.1627	0.9403	-0.0775	-0.7294	-0.0486	0.1674	0.0533	0.1305	0.2695	0.0375	0.2989	-38.0181	-7.9025	18.438
5	0.1016	0.0029	-0.1767	0.4887	-0.3501	0.6123	-0.0621	0.0658	-0.0614	0.0417	0.0568	0.1552	0.0512	-0.0363	0.0053	0.1067	0.0159	0.0337	0.1974	0.0112	0.2425	-27.78	-14.1266	9.7813
6	0.2061	-0.3821	0.1639	1.1509	-0.4013	0.4186	-0.033	0.0042	-0.0464	-0.1133	-0.1036	-0.3721	0.0335	0.2224	0.157	0.1002	-0.003	-0.0015	0.2029	0.0185	0.2149	-13.4861	-13.0094	1.7146
7	0.3396	-0.2245	-0.2164	0.4014	-0.3161	1.1254	-0.1065	0.1266	-0.4349	0.1371	0.1074	0.1539	0.3074	0.0232	-0.0375	0.1455	0.0293	0.0153	0.1878	0.0086	0.2711	-19.07	-20.7156	8.1794
8	0.1636	-0.2428	-0.1739	0.5841	-0.4375	1.0201	-0.0091	0.0809	-0.0484	0.0176	0.0334	0.0848	-0.0637	-0.0434	-0.05	0.1108	0.0213	0.0031	0.1882	0.0058	0.215	-25.7264	-8.6746	6.6795
9	1.0846	-0.9452	-0.5632	1.4855	0.1847	0.6158	-0.0679	0.1172	-0.1488	-0.1865	-0.0313	0.4306	-0.1291	-0.1816	0.0195	0.0498	0.0508	-0.0338	0.1447	0.0101	0.1609	-31.6068	-0.6398	-2.5822
10	0.8737	-0.3212	-0.0752	0.791	-0.0376	0.4589	-0.0868	-0.0518	0.0825	0.1764	0.0387	0.0886	-0.3429	0.0032	0.0166	0.2205	0.0246	-0.0004	0.1712	0.0072	0.1561	-21.7222	3.4563	13.5066
11	0.7156	-0.0106	0.5921	0.2217	0.1409	1.2867	-0.2426	-0.4058	0.1734	0.4859	0.2376	0.413	-0.4278	-0.5592	-0.0783	0.3569	0.1975	0.1792	0.4603	0.0296	0.2603	-34.7328	-1.9862	32.77
12	0.171	0.3422	-0.2619	0.8323	-1.0091	2.1175	-0.0044	-0.3647	-0.2446	0.2733	0.1443	0.4638	-0.3348	-0.6062	-0.1889	0.7177	0.12	0.2494	0.8317	0.2125	0.5951	-40.9042	-7.3712	35.4117
13	0.3662	-0.0523	0.2873	0.6589	0.124	0.3747	-0.3657	-0.5844	0.1587	0.4478	0.2247	-0.0584	-0.7884	-0.0865	0.1345	0.623	0.1963	0.0117	0.3887	-0.0392	0.1496	-23.7478	6.4701	35.3971
14	0.6523	1.4047	0.2895	3.0689	0.3239	4.3549	0.0548	0.0757	0.1625	0.2913	0.1899	0.4171	-0.8765	0.5317	-0.1193	0.8434	-0.0234	-0.0442	0.2912	-0.0299	0.3509	-14.2744	14.4288	31.7084
15	1.9663	-0.0744	-0.4647	0.8207	0.0462	0.1245	-0.2679	-0.9207	0.09	0.8579	0.1726	-0.0532	-0.1514	-0.0783	0.1255	0.8099	0.1464	-0.0129	0.4552	-0.0475	0.1502	-19.359	5.2967	45.6263
16	2.0155	-0.4852	0.4112	0.821	-0.1036	0.0894	0.6408	0.7088	-0.0715	-1.0729	-0.1248	0.1419	-0.8093	0.5833	-0.5294	1.1044	-0.0789	0.151	0.5377	-0.0092	0.2723	-3.2811	5.2095	-38.2565
17	0.8557	0.47	-0.4557	0.9981	0.1535	0.5434	-0.0808	0.1054	-0.0243	-0.1737	0.077	-0.0857	-0.1127	-0.1526	-0.0359	0.2499	-0.0048	0.0122	0.2503	0.0104	0.2093	-8.5888	-2.9856	-17.8832
18	1.1038	-0.0297	-0.0823	1.6942	0.3504	0.0732	0.0653	0.5882	-0.2601	-0.7596	-0.0331	-0.2752	-0.1144	-0.2101	-0.0565	0.4017	0.0013	0.0603	0.3099	0.0024	0.2144	-4.2903	-4.7984	-28.9735
19	0.3663	-0.1535	-0.0086	0.1587	0.0111	0.5871	0.096	0.0598	-0.0845	-0.129	0.0471	-0.1056	-0.0721	0.0866	-0.1345	0.2378	-0.0481	0.0277	0.2034	0.0105	0.248	-0.187	0.143	-15.353
20	1.2455	0.2695	0.3106	1.077	0.0659	1.8141	0.0036	-0.0876	-0.3553	0.0354	-0.1195	-0.4431	0.2675	0.3265	0.0697	0.1767	-0.0025	0.0425	0.1967	0.0306	0.2965	0.7794	-9.7781	-18.4855
21	0.1353	0.0058	-0.3847	0.3933	0.2675	1.083	0.0904	-0.1074	0.0653	0.0277	0.0209	-0.2928	-0.1333	0.4707	-0.0635	0.1584	-0.0702	-0.0104	0.2672	0.0036	0.2812	5.2215	-0.5946	1.6086
22	0.206	0.1397	0.4534	1.2042	0.5594	1.1121	-0.1153	-0.0233	-0.0837	0.2004	0.1719	-0.3357	0.012	0.3694	-0.0575	0.1193	-0.011	-0.0618	0.264	0.0037	0.2159	0.9488	-9.2597	13.5164
23	0.2388	-0.1505	-0.3703	0.2785	-0.105	0.637	0.015	-0.0381	0.0827	0.0313	0.0257	-0.0707	-0.1922	0.0773	-0.0235	0.2053	-0.0522	-0.0366	0.2207	-0.0071	0.2324	-2.3715	2.9365	10.0524
24	0.7508	-0.2142	0.0825	0.1467	-0.0795	1.368	0.031	-0.1754	0.3273	0.3734	-0.0373	-0.3392	-0.6123	0.0696	0.0874	0.3791	-0.0987	-0.079	0.2494	-0.066	0.2534	-0.5411	11.951	17.7975
25	0.6111	-0.3933	-0.2286	0.5262	-0.2416	1.219	0.0009	-0.0231	0.1073	-0.0171	-0.0235	0.0193	-0.4287	-0.0399	-0.035	0.2127	-0.0235	-0.0057	0.146	0.0078	0.1771	-11.2372	6.7653	1.905
26	1.5319	-0.0004	-0.9777	0.0792	0.0617	2.2233	0.1911	0.0476	0.3802	-0.1401	0.0089	-0.3224	-0.5678	0.0909	-0.3485	0.2842	-0.0942	0.0965	0.1664	0.0493	0.2495	4.7347	9.1591	-18.7199
27	1.2448	0.0307	0.2063	0.016	-0.2369	1.4837	-0.2765	0.0836	0.4857	-0.2088	0.1386	-0.5149	-0.4608	0.4104	-0.0436	0.4992	-0.2027	0.1338	0.391	-0.047	0.3781	11.381	10.545	-16.9096
28	0.382	-0.2958	-0.2221	0.4231	-0.0512	0.9764	0.0881	0.1035	0.2022	-0.3511	-0.0376	-0.0095	-0.4778	-0.1221	-0.0515	0.3836	0.017	0.0269	0.2167	0.0439	0.2038	-9.9903	9.8721	-19.4807
29	3.229	0.1138	-1.4803	0.4553	-0.0744	2.3942	0.2985	0.3436	0.5503	-0.3298	0.1534	0.4463	-0.8403	-0.4824	-0.345	0.4313	0.1377	0.0233	0.268	0.0527	0.2732	-20.2334	10.34	-19.2407
30	1.8387	0.4352	0.1985	0.8971	0.303	0.1734	-0.1496	0.8586	0.0316	-0.7715	0.1376	0.3005	-0.4604	-0.3028	-0.0292	0.5146	0.0369	-0.0113	0.4065	0.041	0.1916	-11.3397	4.5265	-31.4709

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 13:40)
2	X-RAY DIFFRACTION	2	(chain A and resid 41:69)
3	X-RAY DIFFRACTION	3	(chain A and resid 70:84)
4	X-RAY DIFFRACTION	4	(chain A and resid 85:92)
5	X-RAY DIFFRACTION	5	(chain A and resid 93:127)
6	X-RAY DIFFRACTION	6	(chain A and resid 128:138)
7	X-RAY DIFFRACTION	7	(chain A and resid 139:146)
8	X-RAY DIFFRACTION	8	(chain A and resid 147:175)
9	X-RAY DIFFRACTION	9	(chain A and resid 176:195)
10	X-RAY DIFFRACTION	10	(chain A and resid 196:243)
11	X-RAY DIFFRACTION	11	(chain A and resid 244:265)
12	X-RAY DIFFRACTION	12	(chain A and resid 266:289)
13	X-RAY DIFFRACTION	13	(chain A and resid 290:322)
14	X-RAY DIFFRACTION	14	(chain A and resid 323:331)
15	X-RAY DIFFRACTION	15	(chain A and resid 332:352)
16	X-RAY DIFFRACTION	16	(chain B and resid 1:14)
17	X-RAY DIFFRACTION	17	(chain B and resid 15:29)
18	X-RAY DIFFRACTION	18	(chain B and resid 30:45)
19	X-RAY DIFFRACTION	19	(chain B and resid 46:59)
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23	X-RAY DIFFRACTION	23	(chain B and resid 154:183)
24	X-RAY DIFFRACTION	24	(chain B and resid 184:199)
25	X-RAY DIFFRACTION	25	(chain B and resid 200:244)
26	X-RAY DIFFRACTION	26	(chain B and resid 245:269)
27	X-RAY DIFFRACTION	27	(chain B and resid 270:288)
28	X-RAY DIFFRACTION	28	(chain B and resid 289:322)
29	X-RAY DIFFRACTION	29	(chain B and resid 323:338)
30	X-RAY DIFFRACTION	30	(chain B and resid 339:352)

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