PDB-3kc2: Crystal structure of mitochondrial HAD-like phosphatase from Sacc...

ID or keywords:

Entry

Database: PDB / ID: 3kc2

Title

Crystal structure of mitochondrial HAD-like phosphatase from Saccharomyces cerevisiae

Components

Uncharacterized protein YKR070W

Keywords

HYDROLASE / Had-like / mitochondral protein / PSI / MCSG /

Structural Genomics /

Protein Structure Initiative / Midwest Center for Structural Genomics /

Phosphoprotein

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 /

SAD / Resolution: 1.55 Å

Authors

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

Citation

Journal: To be Published
Title: Crystal structure of mitochondrial HAD-like phosphatase from Saccharomyces cerevisiae
Authors: Nocek, B. / Evdokimova, E. / Kuznetsova, K. / Iakunine, A. / Savchenko, A. / Edwards, A. / Joachimiak, A.

History

Deposition	Oct 20, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 24, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3kc2.cif.gz	158.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3kc2.ent.gz	134.2 KB	Display	PDB format
PDBx/mmJSON format	3kc2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kc/3kc2 ftp://data.pdbj.org/pub/pdb/validation_reports/kc/3kc2	HTTPS FTP

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Related structure data

Similar structure data	4nu5-d 1pqu-2 6juk-d 1ta4-1 2gcg-1 3n7u-3 4ebf-3 6wqi-2 1pqu-1 2yv3-d 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

Deposited unit

A: Uncharacterized protein YKR070W

B: Uncharacterized protein YKR070W

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	143.734, 67.095, 76.899
Angle α, β, γ (deg.)	90.00, 110.45, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Uncharacterized protein YKR070W Mass: 39642.465 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) / References: UniProt: P36151
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 880 / 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: 2.19 Å³/Da / Density % sol: 43.86 %
Crystal grow	Temperature: 293 K / pH: 7.5 Details: 200mM Na,K phosphate, Hepes, 2mM MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 4, 2009 / 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: 1.55→40 Å / Num. obs: 99129 / % possible obs: 99.6 % / Observed criterion σ(I): 1.9 / Redundancy: 3.5 % / R_merge(I) obs: 0.063 / Net I/σ(I): 24.3
Reflection shell	Resolution: 1.55→1.58 Å / Redundancy: 3.5 % / R_merge(I) obs: 0.766 / Mean I/σ(I) obs: 1.9 / % possible all: 98.9

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
HKL-3000		phasing
REFMAC	5.5.0102	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 1.55→40 Å / Cor.coef. F_o:F_c: 0.976 / Cor.coef. F_o:F_c free: 0.969 / SU B: 2.597 / SU ML: 0.042 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.067 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.169	4956	5 %	RANDOM
R_work	0.144	-	-	-
obs	0.145	94110	99.5 %	-
all	-	99100	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 8.85 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.32 Å²	0 Å²	-1.05 Å²
2-	-	-0.08 Å²	0 Å²
3-	-	-	-0.32 Å²

Refinement step

Cycle: LAST / Resolution: 1.55→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5109	0	23	880	6012

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	5264
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3560
X-RAY DIFFRACTION	r_angle_refined_deg	1.509	1.963	7153
X-RAY DIFFRACTION	r_angle_other_deg	0.935	3	8687
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.078	5	652
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.193	24.286	245
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.469	15	880
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.853	15	30
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	791
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	5851
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1071
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.774	1.5	3229
X-RAY DIFFRACTION	r_mcbond_other	0.247	1.5	1307
X-RAY DIFFRACTION	r_mcangle_it	1.39	2	5223
X-RAY DIFFRACTION	r_scbond_it	2.368	3	2035
X-RAY DIFFRACTION	r_scangle_it	3.666	4.5	1925
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.55→1.59 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.293	350	-
R_work	0.283	6787	-
obs	-	-	97.73 %

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	0.205	0.2587	-0.1009	1.7003	-0.7473	4.2172	0.0227	0.1058	-0.0586	-0.0013	-0.0981	0.0913	-0.0002	-0.1863	0.0754	0.0596	0.0118	-0.0098	0.1157	-0.0298	0.0913	17.09	62.2819	-3.2916
2	0.5004	0.149	-0.9142	1.9873	-0.5642	5.6258	0.0038	0.1894	-0.19	-0.0691	-0.0896	0.2254	0.1164	-0.4835	0.0858	0.0527	-0.0221	-0.0357	0.1675	-0.0805	0.1207	12.0229	56.5844	-7.0006
3	0.9386	-0.3545	0.4203	0.5372	-0.1086	1.7284	0.0802	0.1238	-0.1328	-0.0627	-0.0423	0.0295	0.0797	-0.0575	-0.0379	0.0908	0.0012	-0.0071	0.1081	-0.0286	0.088	23.651	59.3094	-6.2526
4	6.3053	1.9434	2.0431	2.3962	1.785	3.2769	-0.0041	0.0859	-0.241	0.0899	-0.1	0.0597	0.2478	-0.0713	0.1041	0.1033	-0.0235	-0.0094	0.0873	-0.0644	0.0965	21.1101	50.9092	-3.7953
5	0.8361	-0.0857	0.9902	0.1951	0.09	1.3545	0.037	0.1988	-0.0377	-0.0171	-0.0062	0.0038	-0.0238	0.2117	-0.0307	0.0799	0.0014	0.0093	0.1215	-0.0188	0.067	39.6844	61.2441	2.4251
6	1.8726	-0.0592	-0.044	1.0384	0.3817	0.4708	0.0468	0.0451	-0.1126	0.1302	0.0324	-0.0409	0.1019	0.0506	-0.0792	0.113	0	-0.0069	0.0661	-0.0063	0.0873	44.425	57.9878	24.6578
7	6.4012	-1.2466	-3.7584	2.0442	1.5059	8.1434	-0.2547	-0.0597	-0.5239	0.1694	0.0369	0.0823	0.3165	0.3607	0.2178	0.0917	0.0036	0.0072	0.0349	-0.0046	0.1482	39.428	48.1969	20.1256
8	3.6149	2.587	0.331	2.9288	0.317	0.6996	0.0124	0.2491	-0.1886	0.0224	0.1063	-0.1616	0.0367	0.1715	-0.1186	0.063	-0.0027	-0.0021	0.1152	-0.0415	0.0832	51.2425	57.2768	12.751
9	0.4484	-0.0705	0.2736	0.3863	-0.0737	0.6786	-0.0193	0.0788	0.0013	0.0217	0.0154	0.0153	-0.0179	0.0386	0.0039	0.0837	-0.0174	0.0043	0.0722	-0.0027	0.0846	40.4841	66.3823	15.3683
10	2.9313	-1.3409	0.5967	3.7223	2.36	1.7878	-0.1054	0.1741	0.2124	-0.0846	0.0858	-0.1637	-0.1401	0.1246	0.0197	0.0672	-0.0317	-0.0134	0.0715	-0.0013	0.0755	52.4563	73.0448	19.0333
11	1.562	0.9129	1.1582	1.8169	0.8115	1.6752	-0.0257	0.1995	0.14	-0.0219	-0.0493	-0.042	-0.0516	0.1258	0.075	0.093	-0.0259	-0.0106	0.078	0.0306	0.0777	41.5485	75.2739	11.1327
12	1.1718	0.2791	0.2571	0.2728	0.0782	0.5865	-0.0622	0.0667	0.0663	-0.0127	0.018	0.0103	-0.0639	-0.0073	0.0442	0.1006	-0.0127	0	0.0539	0.0093	0.0856	29.5943	72.2566	14.952
13	0.4102	-0.3112	0.1245	1.9197	1.1869	2.1271	0.0658	0.1523	0.0441	-0.1402	-0.1096	-0.049	-0.1726	0.1072	0.0438	0.084	0.0128	0.0062	0.1058	0.0132	0.0616	28.685	70.7929	-7.9418
14	1.8823	-2.438	-0.1397	14.9631	3.4714	3.0824	0.0806	0.3542	0.0525	-0.8327	0.0364	0.0322	0.0645	0.4037	-0.117	0.16	0.0482	-0.0037	0.1813	-0.0029	0.0126	25.4308	67.9025	-19.6972
15	0.4796	0.1876	-0.4937	0.6817	-0.4334	1.684	0.0603	0.0768	0.0394	-0.0545	-0.0373	0.091	-0.117	-0.1279	-0.023	0.0902	0.0309	0.0022	0.1026	0.0065	0.0756	17.3155	73.1806	-4.016
16	4.074	0.6434	-5.1167	4.4362	-3.3227	19.2965	0.3745	-0.1612	0.41	0.3958	-0.0029	0.1091	-1.538	0.03	-0.3716	0.177	0.0683	0.0287	0.0849	-0.0273	0.1667	10.964	78.19	5.1868
17	0.839	0.4655	1.3345	-0.4458	0.7065	3.336	0.0966	0.1639	-0.0217	0.0521	-0.1116	0.1518	0.0425	-0.5286	0.015	0.0476	0.0347	-0.0216	0.3017	-0.0563	0.2269	6.7424	66.2863	-4.321
18	17.3324	5.4383	24.5128	28.3752	-1.3798	30.9102	-0.8397	0.5109	1.0542	-1.0461	-0.0315	0.9073	-0.6586	0.5609	0.8712	0.0773	0.008	-0.0922	0.3613	0.1543	0.2469	7.0629	70.4973	-13.5575
19	0.8166	-0.4023	0.1774	1.6717	1.3736	4.142	-0.0544	-0.158	-0.0066	-0.0099	0.0245	0.0076	0.0755	0.0401	0.0299	0.0798	0.0273	0.0009	0.0949	0.0002	0.0809	46.5291	66.136	46.6683
20	1.83	-0.3748	0.5901	0.3226	-0.1677	1.327	-0.0334	-0.2835	-0.118	0.015	0.0674	0.0286	0.0529	0.0162	-0.0339	0.0799	0.0326	0.0095	0.1188	0.017	0.0697	48.1357	64.4475	53.405
21	3.0165	-0.3742	1.2721	0.7661	-0.518	1.1079	0.0075	-0.117	-0.3337	0.018	0.0233	-0.0032	0.1975	-0.0121	-0.0309	0.1174	0.0309	0.0158	0.0771	0.0466	0.1179	41.015	55.4617	47.9459
22	0.8031	0.1122	0.5414	0.2511	0.0441	0.5635	-0.0392	-0.1779	-0.068	0.0436	0.0068	0.0181	0.0497	-0.1035	0.0324	0.0933	0.0024	0.0281	0.0992	0.0186	0.0776	25.6593	62.0537	43.4345
23	0.5674	0.0778	0.3539	0.429	0.8294	1.8593	0.0501	-0.1092	-0.1114	0.0318	-0.0003	0.0765	0.058	-0.134	-0.0498	0.1078	-0.0226	0.0288	0.0869	0.0372	0.0995	20.4595	56.0789	36.427
24	3.6269	0.6381	-0.1325	0.7037	-0.5528	0.5691	0.0165	0.1543	-0.117	-0.0542	0.0138	-0.0059	0.1503	-0.0275	-0.0303	0.1346	-0.026	0.008	0.0632	-0.0038	0.1002	21.3971	56.0035	19.1813
25	4.5877	1.4226	-4.7287	3.2908	-1.0711	5.389	-0.1004	-0.0156	-0.2702	-0.038	0.0033	-0.0397	0.2496	-0.0268	0.0971	0.0953	-0.0227	0.002	0.0449	0.0151	0.1249	27.2278	47.9941	27.0622
26	2.6691	1.2029	1.3423	3.1664	-0.8637	1.1559	0.0806	-0.1326	-0.089	0.0877	0.0209	0.0334	0.0421	-0.1641	-0.1015	0.0852	-0.0452	0.0268	0.1143	0.0131	0.1002	11.1864	56.0854	32.1419
27	0.6278	-0.2157	0.0778	0.2127	0.0888	0.6743	-0.0044	-0.0293	-0.0087	0.0082	-0.0047	-0.0088	0.0238	-0.0405	0.0091	0.0848	-0.0086	0.0147	0.0669	0.0028	0.0958	24.2411	64.5795	29.0061
28	1.9053	1.9133	0.8946	5.8492	-1.3909	2.2131	-0.1483	-0.0663	0.1487	-0.0392	0.1839	0.4299	-0.1279	-0.3095	-0.0356	0.063	0.0229	-0.0101	0.109	-0.0048	0.1139	9.8871	69.2397	24.7463
29	0.8002	-0.1351	0.2323	0.3301	0.0762	0.304	-0.0676	-0.0538	0.0926	0.0108	0.0108	0.0223	-0.0316	-0.0221	0.0567	0.0944	0.0085	-0.0008	0.0637	-0.0053	0.0847	29.7522	72.8194	30.0085
30	1.5775	-0.2849	-1.4212	1.848	-0.4785	2.9816	-0.0479	-0.1576	0.0796	0.075	0.0475	0.065	-0.0698	-0.0703	0.0005	0.0786	0.0427	0.004	0.1038	-0.0144	0.0715	32.1999	74.507	47.9322
31	3.4762	-3.2299	-0.6968	10.878	-0.2595	7.5689	-0.1577	-0.5368	-0.0828	0.7771	0.1065	0.2533	-0.3019	-0.354	0.0513	0.1247	0.0688	0.0291	0.2377	0.0267	0.008	34.5601	68.0179	60.0519
32	5.5074	5.6771	-2.8596	19.6255	-9.5791	7.0217	0.2845	-0.8056	0.19	0.718	-0.0531	0.3848	0.0045	0.2362	-0.2313	0.2648	0.0766	-0.015	0.2584	-0.0492	0.0325	39.9402	71.0605	63.2485
33	1.0706	-0.4926	-0.6921	0.5188	0.2359	1.3629	-0.0786	-0.103	0.1421	0.0215	0.0533	-0.036	-0.0882	-0.0119	0.0253	0.089	0.0248	-0.0146	0.0837	-0.0263	0.0902	44.521	77.1882	45.2585
34	3.8647	0.2388	-3.0399	2.2909	1.2147	10.677	0.0927	0.1839	0.5044	-0.1429	0.0275	0.0103	-0.856	-0.3801	-0.1201	0.1161	0.0229	-0.0353	0.0216	-0.0012	0.1468	49.2029	83.1107	39.7896
35	2.3898	0.3491	0.8299	0.6519	-0.3612	0.6879	-0.0484	-0.1759	0.1092	-0.0419	-0.0275	0.0153	0.0208	-0.0171	0.0759	0.0814	0.0293	-0.0233	0.1125	-0.0184	0.0865	55.5813	72.5644	49.3223
36	13.9398	9.0485	7.7944	21.2987	2.7016	10.0716	-0.401	-0.6859	0.7702	0.3458	0.0043	0.3525	-0.4985	-0.2915	0.3967	0.1238	0.0632	-0.0178	0.2493	-0.1407	0.1125	54.5903	78.196	58.2246

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	12 - 29
2	X-RAY DIFFRACTION	2	A	30 - 42
3	X-RAY DIFFRACTION	3	A	43 - 62
4	X-RAY DIFFRACTION	4	A	63 - 72
5	X-RAY DIFFRACTION	5	A	73 - 122
6	X-RAY DIFFRACTION	6	A	123 - 134
7	X-RAY DIFFRACTION	7	A	135 - 142
8	X-RAY DIFFRACTION	8	A	143 - 154
9	X-RAY DIFFRACTION	9	A	155 - 181
10	X-RAY DIFFRACTION	10	A	182 - 191
11	X-RAY DIFFRACTION	11	A	192 - 204
12	X-RAY DIFFRACTION	12	A	205 - 244
13	X-RAY DIFFRACTION	13	A	245 - 262
14	X-RAY DIFFRACTION	14	A	263 - 285
15	X-RAY DIFFRACTION	15	A	286 - 322
16	X-RAY DIFFRACTION	16	A	323 - 334
17	X-RAY DIFFRACTION	17	A	335 - 346
18	X-RAY DIFFRACTION	18	A	347 - 352
19	X-RAY DIFFRACTION	19	B	13 - 29
20	X-RAY DIFFRACTION	20	B	30 - 54
21	X-RAY DIFFRACTION	21	B	55 - 74
22	X-RAY DIFFRACTION	22	B	75 - 108
23	X-RAY DIFFRACTION	23	B	109 - 124
24	X-RAY DIFFRACTION	24	B	125 - 134
25	X-RAY DIFFRACTION	25	B	135 - 145
26	X-RAY DIFFRACTION	26	B	146 - 155
27	X-RAY DIFFRACTION	27	B	156 - 180
28	X-RAY DIFFRACTION	28	B	181 - 192
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