PDB-2npm: crystal structure of Cryptosporidium parvum 14-3-3 protein in com...

ID or keywords:

Entry

Database: PDB / ID: 2npm

Title

crystal structure of Cryptosporidium parvum 14-3-3 protein in complex with peptide

Components

14-3-3 domain containing protein
CONSENSUS PEPTIDE FOR 14-3-3 PROTEINS

Keywords

PROTEIN BINDING / cell regulator protein 14-3-3 /

Cryptosporidium parvum /

Structural genomics /

Structural Genomics Consortium / SGC

Function / homology

Function and homology information

14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. /

14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily /

14-3-3 protein ...
Similarity search - Domain/homology

Biological species

Cryptosporidium parvum (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.52 Å

Authors

Dong, A. / Lew, J. / Wasney, G. / Ren, H. / Lin, L. / Hassanali, A. / Qiu, W. / Zhao, Y. / Doyle, D. / Vedadi, M. ...

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	Oct 27, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 7, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Feb 22, 2012	Group: Database references
Revision 1.4	Oct 18, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.5	Aug 30, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2npm.cif.gz	195 KB	Display	PDBx/mmCIF format
PDB format	pdb2npm.ent.gz	157 KB	Display	PDB format
PDBx/mmJSON format	2npm.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/np/2npm ftp://data.pdbj.org/pub/pdb/validation_reports/np/2npm	HTTPS FTP

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Related structure data

Related structure data	2o8pC 3efzC 1ywtS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5d3e-2 6ylu-1 6y3o-1 6yp3-1 6qhm-1 6y3w-1 6yp8-1 6gkg-1 6qhl-1 2c74-d 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 (8)

Deposited unit

A: 14-3-3 domain containing protein

X: CONSENSUS PEPTIDE FOR 14-3-3 PROTEINS

B: 14-3-3 domain containing protein

Y: CONSENSUS PEPTIDE FOR 14-3-3 PROTEINS

61 kDa, 4 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)	104.125, 104.125, 148.877
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	14-3-3 domain containing protein Mass: 29771.598 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Gene: cgd3_1290 / Plasmid: p15-tev-lic DERIVED FROM PET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta-R3 / References: UniProt: Q5CUW0
#2: Protein/peptide	CONSENSUS PEPTIDE FOR 14-3-3 PROTEINS Mass: 736.774 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 107 / 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: 3.31 Å³/Da / Density % sol: 62.8 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 14% PEG 3350, 0.1 M Calcium Acetate, 0.2 M Trimethylamine-N-oxide, 0.1 M Hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 22, 2006
Radiation	Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.52→50 Å / Num. all: 28423 / Num. obs: 28423 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.3 % / B_iso Wilson estimate: 71.9 Å² / R_merge(I) obs: 0.063 / R_sym value: 0.063 / Net I/σ(I): 10.4
Reflection shell	Resolution: 2.52→2.56 Å / Redundancy: 13.1 % / R_merge(I) obs: 0.981 / Mean I/σ(I) obs: 2.36 / Num. unique all: 1400 / R_sym value: 0.981 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
JDirector		data collection
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing
Coot	0.1	model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1YWT

1ywt

Resolution: 2.52→42.68 Å / Cor.coef. F_o:F_c: 0.941 / Cor.coef. F_o:F_c free: 0.929 / SU B: 17.491 / SU ML: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.304 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27541	599	2.1 %	RANDOM
R_work	0.22065	-	-	-
all	0.22174	27756	-	-
obs	0.22174	27756	99.89 %	-

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: 28.693 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.51 Å²	0 Å²	0 Å²
2-	-	-0.51 Å²	0 Å²
3-	-	-	1.02 Å²

Refinement step

Cycle: LAST / Resolution: 2.52→42.68 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3649	0	0	107	3756

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.021	3706
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.498	1.963	5029
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.895	5	478
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.336	24.494	158
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.675	15.05	601
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.032	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.096	0.2	584
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	2770
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.223	0.2	1722
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.304	0.2	2573
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.137	0.2	176
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	0.203	0.2	12
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.134	0.2	7
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	0.696	1.5	2479
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.162	2	3821
X-RAY DIFFRACTION	r_scbond_it	1.966	3	1401
X-RAY DIFFRACTION	r_scangle_it	2.879	4.5	1208
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.52→2.584 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.416	36	-
R_work	0.347	2036	-
obs	-	-	99.95 %

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	7.248	-3.2627	-0.0906	5.4986	-1.6074	2.7606	0.4628	0.7563	-1.6054	-0.5155	-0.2637	1.2138	0.4748	-0.3149	-0.1992	0.2254	0.1485	-0.1006	0.1948	-0.1854	0.5632	8.6633	16.8157	25.1355
2	6.8321	2.2611	1.8055	4.331	0.7471	0.4834	0.1732	0.1842	-0.2701	-0.1448	-0.4104	0.1832	-0.0177	0.0752	0.2371	0.32	0.1736	0.0132	0.2907	-0.0011	0.2754	13.0188	29.4108	30.688
3	10.8655	-3.9998	-7.8493	5.4248	3.9292	5.9439	-0.1559	-0.0023	0.744	0.3531	0.1099	-0.2404	-0.1068	-0.202	0.046	0.296	0.1506	0.0483	0.176	0.1917	0.3636	22.6281	44.5996	32.3056
4	13.7662	7.7214	0.6131	17.8351	11.8395	19.536	0.3773	0.1605	1.9837	-0.6789	-0.9454	-0.8448	-2.389	0.7942	0.5682	0.4102	-0.0056	0.1425	-0.0518	0.2003	0.9687	29.5875	54.3616	30.2109
5	14.0496	4.9273	1.6162	5.5029	1.9582	0.6988	0.0412	1.1962	0.0318	-0.868	-0.2163	-0.2341	-0.1055	0.0553	0.1751	0.3894	0.2183	0.0813	0.4011	0.134	0.1757	15.4769	37.6821	22.6407
6	12.7053	-7.9882	3.4768	8.3187	1.9465	6.1322	0.4892	0.745	-1.7473	-0.5119	-0.3298	1.4243	0.3649	-0.9373	-0.1594	0.1299	0.0304	-0.2293	0.3047	-0.1929	0.6263	-5.8504	26.123	25.6751
7	5.9467	-1.5593	0.5307	3.7494	-0.2188	2.2741	0.2011	0.2199	-0.3551	-0.1042	-0.1812	0.3752	-0.225	-0.4832	-0.0199	0.2621	0.1561	0.0121	0.3157	0.0476	0.2216	-0.4016	37.6874	33.2305
8	1.9304	-2.2693	-0.1028	4.6436	-3.1443	8.9983	-0.1981	-0.4254	0.212	0.3377	0.5265	0.3446	-0.5971	-1.2733	-0.3284	0.2856	0.2703	0.0278	0.4908	0.0645	0.0647	-2.2626	43.0944	45.2278
9	0.4717	3.1955	3.4436	38.6741	6.0883	42.594	0.3196	-0.3773	0.1652	0.1054	-1.1222	0.5134	2.5262	0.2034	0.8026	0.3816	0.0983	0.1304	0.7681	0.154	0.6046	-3.7442	23.1439	51.5351
10	6.8302	-0.8965	1.5565	5.8502	-0.4768	4.1852	-0.1868	-1.0453	0.0457	0.5254	0.1912	-0.0862	-0.2358	0.2443	-0.0044	0.3118	0.1985	0.0157	0.4508	0.1335	0.1052	5.8762	37.335	47.4166
11	9.5237	0.479	-1.4729	9.3475	-0.2655	4.373	0.2263	0.7448	1.191	-0.3951	-0.3483	-0.7545	-0.2847	0.3807	0.122	0.1859	0.1735	0.1245	0.2421	0.2783	0.3926	35.4386	38.5016	25.9115
12	10.6141	-2.9983	4.0289	9.678	1.7851	11.0936	0.3715	1.3442	1.726	-0.3133	-0.072	-1.6313	-0.696	0.5825	-0.2995	0.0892	0.0641	0.2511	0.2793	0.3315	0.6715	48.0827	36.5548	25.7929
13	5.0299	1.2498	-0.3313	7.0588	-0.2004	0.0239	0.2691	0.2169	-0.2662	-0.1416	-0.392	-0.0066	0.1407	0.0705	0.1229	0.3846	0.2002	0.0317	0.3523	0.026	0.2401	31.4711	19.5977	30.447
14	19.7716	18.1317	4.2755	32.3833	-8.3996	29.404	0.8009	0.3562	-2.4971	-0.298	-0.4904	-0.6476	2.1696	-1.7785	-0.3105	0.3006	0.1568	-0.1162	-0.1065	-0.1395	0.7948	18.5265	1.842	28.5443
15	9.1496	1.9572	-0.3146	4.445	-0.3336	0.7915	0.1869	0.8298	0.5587	-0.6987	-0.3137	-0.2373	0.0414	0.3709	0.1268	0.3618	0.2413	0.1301	0.4455	0.1039	0.1994	41.4437	22.3656	23.6237
16	4.8403	-0.5455	0.2565	3.288	0.0963	2.7162	0.1755	0.4049	0.0394	-0.2562	-0.175	-0.4482	0.1544	0.5732	-0.0005	0.2671	0.2096	0.0915	0.4036	0.0707	0.2487	48.69	17.0265	31.7094
17	5.2822	1.6952	3.8564	3.9972	-0.8755	17.6528	0.2869	0.1881	-0.3558	-0.2382	-0.4957	0.2519	0.5581	-0.0052	0.2089	0.306	0.2653	0.0396	0.3321	0.0051	0.2121	46.4034	6.0598	38.0247
18	2.9814	5.5283	6.9261	24.2852	20.6361	38.1428	0.2464	0.2303	0.0371	0.7113	0.1263	-1.1071	-0.5588	1.7433	-0.3726	0.186	0.109	0.0126	0.3969	0.0432	0.1392	55.092	18.3461	49.7203
19	24.9184	6.2273	9.0564	19.819	5.4658	13.401	0.004	0.853	2.177	0.8951	-0.5344	-0.831	-1.8279	-0.1041	0.5304	0.4664	0.1845	0.019	0.2015	0.0625	0.2088	47.9545	28.067	50.2037
20	7.5708	-4.5873	2.3456	4.4402	0.9618	6.9431	-0.1714	-0.3754	-0.4041	0.3424	0.1967	0.152	0.5744	-0.6719	-0.0253	0.254	0.1435	0.0512	0.3369	0.0161	0.1483	41.6674	13.9317	45.3537

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	21 - 69	21 - 69
2	X-RAY DIFFRACTION	2	A	A	70 - 86	70 - 86
3	X-RAY DIFFRACTION	3	A	A	87 - 94	87 - 94
4	X-RAY DIFFRACTION	4	A	A	95 - 107	95 - 107
5	X-RAY DIFFRACTION	5	A	A	108 - 131	108 - 131
6	X-RAY DIFFRACTION	6	A	A	132 - 144	132 - 144
7	X-RAY DIFFRACTION	7	A	A	145 - 208	145 - 208
8	X-RAY DIFFRACTION	8	A	A	209 - 231	209 - 231
9	X-RAY DIFFRACTION	9	A	A	232 - 242	232 - 242
10	X-RAY DIFFRACTION	10	A	A	243 - 259	243 - 259
11	X-RAY DIFFRACTION	11	B	C	24 - 54	24 - 54
12	X-RAY DIFFRACTION	12	B	C	55 - 70	55 - 70
13	X-RAY DIFFRACTION	13	B	C	71 - 94	71 - 94
14	X-RAY DIFFRACTION	14	B	C	95 - 108	95 - 108
15	X-RAY DIFFRACTION	15	B	C	109 - 147	109 - 147
16	X-RAY DIFFRACTION	16	B	C	148 - 206	148 - 206
17	X-RAY DIFFRACTION	17	B	C	207 - 218	207 - 218
18	X-RAY DIFFRACTION	18	B	C	219 - 235	219 - 235
19	X-RAY DIFFRACTION	19	B	C	236 - 248	236 - 248
20	X-RAY DIFFRACTION	20	B	C	249 - 259	249 - 259

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