PDB-3efz: Crystal Structure of a 14-3-3 protein from cryptosporidium parvum...

ID or keywords:

Entry

Database: PDB / ID: 3efz

Title

Crystal Structure of a 14-3-3 protein from cryptosporidium parvum (cgd1_2980)

Components

14-3-3 protein

Keywords

SIGNALING PROTEIN / 14-3-3 / cell regulation / Structural Genomics / Structural Genomics Consortium / SGC

Function / homology

Function and homology information

14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology

Biological species

Cryptosporidium parvum (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.08 Å

Authors

Wernimont, A.K. / Dong, A. / Qiu, W. / Lew, J. / Wasney, G.A. / Vedadi, M. / Kozieradzki, I. / Zhao, Y. / Ren, H. / Alam, Z. ...

Citation

Journal: Plos One / Year: 2011
Title: Characterization of 14-3-3 proteins from Cryptosporidium parvum.
Authors: Brokx, S.J. / Wernimont, A.K. / Dong, A. / Wasney, G.A. / Lin, Y.H. / Lew, J. / Vedadi, M. / Lee, W.H. / Hui, R.

History

Deposition	Sep 10, 2008	Deposition site: RCSB / Processing site: RCSB
Supersession	Sep 23, 2008	ID: 2IJP
Revision 1.0	Sep 23, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Feb 22, 2012	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3efz.cif.gz	189.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3efz.ent.gz	158.9 KB	Display	PDB format
PDBx/mmJSON format	3efz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3efz_validation.pdf.gz	488.8 KB	Display	wwPDB validaton report
Full document	3efz_full_validation.pdf.gz	503.5 KB	Display
Data in XML	3efz_validation.xml.gz	36.4 KB	Display
Data in CIF	3efz_validation.cif.gz	52.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ef/3efz ftp://data.pdbj.org/pub/pdb/validation_reports/ef/3efz	HTTPS FTP

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Related structure data

Related structure data	2npmC 2o8pC C: citing same article (ref.)
Similar structure data	3gmq-d 1ktd-1 2wtz-1 5ibm-1 6cpo-2 6bmr-2 4h25-1 5fqf-1 4mcz-d 4u43-d 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 - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#222 - Jun 2018 Proteins and Nanoparticles similarity (5)

Deposited unit

A: 14-3-3 protein

B: 14-3-3 protein

C: 14-3-3 protein

D: 14-3-3 protein

hetero molecules

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

1

A: 14-3-3 protein

B: 14-3-3 protein

hetero molecules

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

2

C: 14-3-3 protein

D: 14-3-3 protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	76.464, 106.712, 92.513
Angle α, β, γ (deg.)	90.00, 112.83, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	14-3-3 protein Mass: 31030.000 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Gene: cgd1_2980 / Plasmid: PET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-rosetta-oxford / References: UniProt: Q5CSF3
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 420 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 2.8 Å³/Da / Density % sol: 56.11 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 3350, 0.2 M Ammoniuim Formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1
1,2		1

Diffraction source

Source	Site	Beamline	Type	ID	Wavelength (Å)
ROTATING ANODE			RIGAKU FR-E+ SUPERBRIGHT	1	1.5418
SYNCHROTRON	APS	22-ID		2	0.97625

Detector

Type	ID	Detector	Date
RIGAKU RAXIS IV++	1	IMAGE PLATE	Sep 22, 2006
ADSC QUANTUM 4	2	CCD	Jul 14, 2006

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SINGLE WAVELENGTH	M	x-ray	1
2	SINGLE WAVELENGTH	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.5418	1
2	0.97625	1

Reflection

Resolution: 2.08→50 Å / Num. obs: 77311 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / R_sym value: 0.106 / Net I/σ(I): 16.4

Reflection shell

Resolution: 2.08→2.18 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.18 / R_sym value: 0.93 / % possible all: 100

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
SOLVE		phasing
REFMAC	5.2.0019	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.08→25 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.922 / SU B: 10.549 / SU ML: 0.146 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.19 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26716	4081	5 %	RANDOM
R_work	0.22498	-	-	-
obs	0.22715	77311	99.3 %	-
all	-	77854	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 37.594 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.52 Å²	0 Å²	-0.1 Å²
2-	-	1.6 Å²	0 Å²
3-	-	-	-2.2 Å²

Refinement step

Cycle: LAST / Resolution: 2.08→25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6947	0	24	420	7391

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	7150
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.246	1.992	9603
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.204	5	887
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.323	25.156	353
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.013	15.021	1431
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.058	15	52
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	1091
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	5250
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.199	0.2	3597
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.295	0.2	5027
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.164	0.2	392
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	0.172	0.2	48
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.176	0.2	17
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	0.516	1.5	4539
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.801	2	7013
X-RAY DIFFRACTION	r_scbond_it	1.587	3	2941
X-RAY DIFFRACTION	r_scangle_it	2.44	4.5	2577
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.08→2.135 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.361	273	-
R_work	0.313	5301	-
obs	-	-	92.64 %

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	18.6221	-11.5989	-2.0188	14.8562	12.9758	18.2124	0.4473	2.1718	-0.1785	-1.7984	-0.6379	0.618	-0.2403	-0.3535	0.1906	0.4101	-0.0943	-0.016	0.5055	0.1574	0.3909	-21.9935	-5.4051	-57.438
2	1.4733	-0.1514	-0.1597	6.6274	-3.3994	2.892	-0.0114	-0.0163	-0.1248	0.1396	-0.0764	-0.0443	0.0485	0.0434	0.0878	-0.0922	0.0286	0.0557	-0.071	-0.0164	-0.0631	-19.6818	-18.2293	-32.5747
3	4.3577	-0.0472	-0.1705	1.6348	0.0638	2.0615	0.0893	0.3069	0.3366	-0.0569	-0.0656	0.0764	-0.2642	-0.0964	-0.0237	-0.0455	0.0384	0.0292	-0.1074	-0.0153	-0.0124	-33.166	-2.0843	-35.4735
4	5.3288	-1.0617	-0.5204	3.388	-0.2314	2.7939	0.1559	0.3351	-0.3346	-0.1918	-0.1311	0.1753	0.3678	-0.2448	-0.0248	0.0059	0.0138	-0.0314	-0.0059	-0.0747	0.0946	-45.6913	-12.4374	-38.5168
5	0.7305	1.7232	-5.4303	4.0647	-12.8094	40.3669	-0.0469	-1.2775	-1.4293	1.9044	-0.1703	-0.3273	-1.2531	1.9786	0.2172	0.4541	-0.0776	-0.0535	0.6263	0.1317	0.3602	-7.7461	-6.8541	-26.2258
6	6.6206	3.8615	-1.347	9.4909	-2.7584	7.4889	-0.133	0.445	0.5401	-0.5842	0.0134	-0.1416	-0.3678	0.0106	0.1196	-0.0168	0.029	0.0536	0.0052	0.0224	0.0088	-10.4963	-0.2573	-47.6974
7	1.9654	1.4958	-1.3313	4.5504	-2.9142	3.1268	-0.2017	-0.0658	-0.4706	-0.1788	-0.0599	-0.182	0.5286	0.204	0.2616	-0.0203	0.0413	0.0872	-0.0594	-0.017	0.0782	-12.3806	-26.6588	-37.1612
8	2.1665	-0.2402	-0.1821	2.6264	-1.2824	2.3578	-0.0455	0.0871	-0.0189	-0.1476	-0.1508	-0.2254	-0.0436	0.1314	0.1963	-0.0534	-0.0038	0.0283	0.0357	0.0196	-0.0429	2.0991	-8.5916	-49.1477
9	3.551	1.0921	0.3071	10.8847	3.47	3.5298	-0.052	-0.4227	0.048	0.9231	0.0146	-0.8428	-0.081	0.0154	0.0374	0.1065	0.036	-0.1651	0.2902	0.0867	0.1189	11.7791	-4.9889	-34.5797
10	12.0215	-13.1724	-5.4498	14.5631	7.699	25.507	-1.2191	-1.2299	-1.7787	1.7579	1.0282	0.3593	1.6121	1.1621	0.1909	0.5467	-0.0312	-0.0603	0.5724	0.0999	0.3937	11.2303	-12.6043	-27.767
11	11.0571	2.2795	-7.3956	8.179	-10.7723	16.0398	0.3001	0.4626	0.529	-0.1514	0.2078	-0.8823	-0.1254	1.5772	-0.5079	0.5153	-0.0332	0.1436	0.5553	-0.0996	0.4158	-26.0816	11.4024	-9.4029
12	1.8311	-2.7465	-0.8361	6.5166	2.0326	2.3744	0.0416	0.0269	0.0115	-0.0922	-0.0655	0.0295	-0.0269	0.0402	0.0239	-0.0048	0.0062	-0.007	-0.0275	0.0296	-0.1216	-45.5651	22.541	6.7334
13	4.6581	-1.236	0.773	3.1339	0.0424	3.1209	0.1482	0.2913	-0.3125	-0.1038	-0.2207	-0.3106	0.4289	0.441	0.0725	0.0897	0.048	0.019	-0.043	0.0428	-0.0204	-33.3484	6.7728	13.8169
14	3.0116	0.1269	0.5598	4.5497	0.1664	4.8906	0.1225	0.0216	0.3005	0.1751	-0.274	-0.6967	-0.1794	0.5967	0.1515	0.0468	-0.0064	-0.0335	0.0767	0.1036	0.1622	-25.6728	17.4564	22.4309
15	3.6843	0.8911	-0.0141	5.1258	3.2272	10.1199	0.1341	0.0024	-0.3217	-0.0574	-0.2779	0.2782	0.3514	-0.3255	0.1438	0.1474	0.0267	-0.0055	-0.0097	0.0306	-0.0293	-45.5942	6.7049	-6.626
16	0.7086	-0.0048	-0.1921	1.4698	1.9109	3.6135	-0.003	0.1021	0.067	-0.257	-0.089	-0.039	-0.495	-0.037	0.0921	0.1036	0.0427	0.0111	-0.0013	0.0361	-0.0409	-46.3603	23.1197	-11.4877
17	3.3715	-0.1835	-0.0949	5.5399	0.5827	4.9567	0.0446	0.1039	-0.055	-0.061	-0.2078	0.5567	0.0079	-0.627	0.1633	0.0013	0.033	-0.0111	0.2233	-0.0783	0.0187	-58.7583	10.772	-20.406
18	6.2149	0.3645	0.9606	10.0957	-1.0709	10.8114	0.0264	-0.2468	-0.1537	0.6999	-0.1998	0.993	0.1937	-0.9641	0.1733	0.1305	-0.0579	0.067	0.4998	-0.0985	0.2458	-66.5433	6.1663	-13.4224

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	46 - 64
2	X-RAY DIFFRACTION	2	A	65 - 129
3	X-RAY DIFFRACTION	3	A	130 - 215
4	X-RAY DIFFRACTION	4	A	216 - 268
5	X-RAY DIFFRACTION	5	B	30 - 42
6	X-RAY DIFFRACTION	6	B	43 - 72
7	X-RAY DIFFRACTION	7	B	73 - 119
8	X-RAY DIFFRACTION	8	B	120 - 205
9	X-RAY DIFFRACTION	9	B	206 - 246
10	X-RAY DIFFRACTION	10	B	247 - 258
11	X-RAY DIFFRACTION	11	C	45 - 64
12	X-RAY DIFFRACTION	12	C	65 - 130
13	X-RAY DIFFRACTION	13	C	131 - 206
14	X-RAY DIFFRACTION	14	C	207 - 268
15	X-RAY DIFFRACTION	15	D	33 - 72
16	X-RAY DIFFRACTION	16	D	73 - 176
17	X-RAY DIFFRACTION	17	D	177 - 218
18	X-RAY DIFFRACTION	18	D	219 - 254

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