PDB-5z81: Trimeric structure of Vibrio cholerae Heat Shock Protein 15 at 2....

ID or keywords:

Entry

Database: PDB / ID: 5z81

Title

Trimeric structure of Vibrio cholerae Heat Shock Protein 15 at 2.3 Angstrom resolution

Components

Heat shock protein 15

Heat shock response

Keywords

CHAPERONE /

Heat shock protein /

RNA binding / Alpha-L motif / Trimer

Function / homology

Function and homology information

ribosomal large subunit binding / cellular response to heat /

single-stranded RNA binding /

Biological species

Vibrio cholerae serotype O1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.334 Å

Authors

Roy Chowdhury, S. / Sen, U.

Citation

Journal: To Be Published
Title: Trimeric structure of Vibrio cholerae Heat Shock Protein 15 at 2.3 Angstrom resolution
Authors: Roy Chowdhury, S. / Sen, U.

History

Deposition	Jan 30, 2018	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 7, 2018	Provider: repository / Type: Initial release
Revision 1.1	Mar 27, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5z81.cif.gz	142.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5z81.ent.gz	113.2 KB	Display	PDB format
PDBx/mmJSON format	5z81.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z8/5z81 ftp://data.pdbj.org/pub/pdb/validation_reports/z8/5z81	HTTPS FTP

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Related structure data

Similar structure data	6qjd-d 3b8l-2 2q1m-1 3h6x-d 5rb1-1 2okd-d 4e4s-1 2baz-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#32 - Aug 2002 Chaperones similarity (1)

Deposited unit

A: Heat shock protein 15

B: Heat shock protein 15

C: Heat shock protein 15

hetero molecules

45.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	53.650, 90.280, 81.090
Angle α, β, γ (deg.)	90.00, 103.92, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-386- HOH
2	1	B-389- HOH
3	1	B-392- HOH

#1: Protein	Heat shock protein 15 / Heat shock response Mass: 14878.106 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: cytoplasm Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395) (bacteria) Strain: ATCC 39541 / Classical Ogawa 395 / O395 / Cell line: XL1Blue / Gene: VC0395_A2308 / Plasmid: pET28 Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) References: UniProt: A0A0H3AM46
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.14 Å³/Da / Density % sol: 42.4 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 2.4M Ammonium Sulphate, 5% MPD.

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Data collection

Diffraction	Mean temperature: 293.15 K
Diffraction source	Source: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.987 Å
Detector	Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Jul 23, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.987 Å / Relative weight: 1
Reflection	Resolution: 2.33→39.35 Å / Num. obs: 15374 / % possible obs: 93 % / Redundancy: 2.02 % / R_merge(I) obs: 0.01 / Net I/σ(I): 5.9
Reflection shell	Resolution: 2.33→2.34 Å

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
iMOSFLM		data reduction
Aimless		data scaling
PHENIX		phasing

Refinement

Resolution: 2.334→39.354 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 23.43 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2594	1538	10 %
R_work	0.2277	-	-
obs	0.2309	15374	96.06 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.334→39.354 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2424	0	39	267	2730

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	2490
X-RAY DIFFRACTION	f_angle_d	1.691	3330
X-RAY DIFFRACTION	f_dihedral_angle_d	19.722	990
X-RAY DIFFRACTION	f_chiral_restr	0.064	348
X-RAY DIFFRACTION	f_plane_restr	0.007	426

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 (%)
2.334-2.4093	0.2978	131	0.2571	1179	X-RAY DIFFRACTION	91
2.4093-2.4954	0.2875	142	0.2582	1270	X-RAY DIFFRACTION	97
2.4954-2.5953	0.2885	139	0.2646	1261	X-RAY DIFFRACTION	97
2.5953-2.7134	0.3116	141	0.2597	1263	X-RAY DIFFRACTION	97
2.7134-2.8564	0.2989	142	0.2607	1279	X-RAY DIFFRACTION	98
2.8564-3.0353	0.3054	141	0.2427	1270	X-RAY DIFFRACTION	97
3.0353-3.2696	0.2609	141	0.23	1263	X-RAY DIFFRACTION	97
3.2696-3.5984	0.26	139	0.2069	1254	X-RAY DIFFRACTION	97
3.5984-4.1186	0.2113	141	0.1942	1279	X-RAY DIFFRACTION	96
4.1186-5.1872	0.2198	141	0.1856	1259	X-RAY DIFFRACTION	96
5.1872-39.3598	0.2438	140	0.2516	1259	X-RAY DIFFRACTION	93

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	1.5258	-0.9077	-0.4996	1.2216	0.974	1.5351	-0.3127	0.3476	-0.793	0.1204	0.2395	0.029	0.5631	0.0261	0.0427	0.3809	0.1401	0.3132	-0.0135	-0.0724	0.4411	-7.0257	18.4204	9.1682
2	6.5203	-3.4803	2.9866	4.377	-0.9629	1.5617	-0.193	-0.2692	-1.2713	-0.0803	0.0364	0.5564	0.2521	-0.065	-0.0513	0.6067	-0.1687	0.1289	0.2384	-0.1009	0.2826	-15.8526	16.3991	11.9314
3	5.4628	1.7118	-1.9929	5.0552	1.2562	6.9502	-0.2737	0.5523	0.2002	-0.4415	-0.1716	0.7828	0.5478	-0.8134	0.2531	0.3492	0.0773	-0.1464	0.1028	0.111	0.1725	-16.7996	24.561	5.0914
4	8.7641	1.2212	0.8481	5.4813	1.4792	7.5653	0.1352	-1.2937	-0.619	1.1462	-0.6414	-0.2828	1.2208	0.0784	0.6082	0.6088	0.0178	-0.0543	0.3191	0.1341	0.4809	-14.406	23.8247	19.6294
5	3.3057	-1.4463	0.6043	4.4888	-0.2089	7.2462	-0.5145	-0.2593	-0.0644	0.5987	0.062	0.134	0.1272	-0.2951	0.3473	0.2651	0.0215	0.0461	0.0817	-0.0347	0.2234	-11.7189	29.2204	15.56
6	3.2606	0.2339	1.1222	1.3904	-0.0837	1.6259	-0.0515	-0.0835	-0.5338	0.0604	0.4023	-0.2024	0.2098	0.4657	-0.1485	0.3061	0.0021	0.154	0.1335	-0.0055	0.199	-0.9951	25.8271	11.0728
7	4.7438	0.4324	0.5809	1.786	0.0866	3.6476	-0.1905	-0.8895	0.0413	1.2251	0.0971	0.8361	-0.2879	0.113	0.0873	0.4908	0.0484	0.0777	0.3607	-0.1215	0.295	-12.9814	33.0805	27.194
8	2.5218	-2.1277	-0.962	3.2774	3.1929	4.6722	0.1718	0.2991	-0.2651	-0.5251	-0.5165	0.3899	-0.3269	-0.5556	0.3222	0.7028	0.2526	0.0056	1.0373	-0.3602	0.5822	-15.5607	27.2671	38.1834
9	2.837	1.0721	-1.9887	4.7576	-1.868	5.368	0.2812	0.3823	0.4625	-0.4609	0.2025	0.5375	-0.477	-0.8211	-0.4711	0.358	0.1274	-0.0215	0.1001	-0.0364	0.2823	-15.8892	50.2924	7.0237
10	9.5798	2.2033	4.1255	1.5662	1.966	5.2597	-0.7084	-0.0384	0.6398	0.3257	0.4076	0.4486	-0.416	0.0567	0.275	0.4923	0.1088	0.1309	0.1502	0.0136	0.3696	-15.7831	58.4094	12.5272
11	3.3279	-0.0364	1.4723	3.7704	-0.7346	1.2249	0.1795	-0.3422	0.2057	0.1247	-0.2248	0.201	-0.6496	-1.0034	0.0006	0.3838	0.2246	0.0749	-0.1098	-0.0403	0.2914	-9.6749	48.0388	11.3696
12	8.5944	-2.4035	-2.1342	1.479	1.6976	2.0284	-0.5095	-1.373	0.1725	1.2146	0.2664	0.367	0.0561	0.143	0.1498	0.739	-0.1054	0.0156	0.4402	0.093	0.3343	-9.7457	44.9162	31.6
13	7.8091	-3.5678	-3.2638	5.9051	0.0519	5.9447	-0.1282	0.0691	0.7969	0.4976	0.0572	-0.6103	-0.5128	0.4056	0.0336	0.3349	-0.1046	-0.008	0.1852	0.0239	0.3103	15.8116	42.1719	14.6259
14	3.4635	-1.8265	4.271	9.6747	-1.353	9.7274	-0.6221	0.4824	0.1212	-0.3336	-0.1252	-1.8341	-0.7015	1.7049	0.6763	0.3026	-0.0849	-0.0031	0.6861	0.1034	0.5187	22.5909	39.3244	20.4427
15	5.6984	0.0736	-1.2749	2.3337	0.5607	2.6616	-0.0534	-0.967	-0.0348	0.9664	-0.0814	-0.1304	0.1956	0.9432	0.0716	0.4716	0.0144	-0.031	0.3241	-0.0119	0.2152	14.2879	31.9249	18.3223
16	2.6986	0.369	-0.3897	5.318	-0.2574	0.7784	0.1513	-0.068	0.3832	-0.1128	-0.1012	0.066	-0.3462	0.1661	-0.0088	0.3215	-0.0222	0.0326	0.1189	-0.0342	0.1543	6.2414	41.5213	14.9973
17	7.5413	2.7054	2.7333	5.0628	4.9019	4.7545	-0.0619	-0.9311	-0.35	1.2125	-0.0774	0.1826	0.7113	0.0246	0.0993	0.5468	0.0368	0.1407	0.2676	-0.0206	0.2899	-0.2914	33.3871	29.1914
18	8.2563	2.8367	-5.9604	6.9099	-4.7587	1.9996	-0.1198	1.052	0.1272	-1.2795	0.1522	-0.2378	0.8661	-0.9175	-0.0099	1.4176	0.049	-0.0614	0.8635	0.2352	0.4117	0.6762	36.7748	41.8046

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 8 through 24 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 25 through 39 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 40 through 54 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 55 through 63 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 64 through 69 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 70 through 89 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 90 through 101 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 102 through 106 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 8 through 24 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 25 through 38 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 39 through 89 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 90 through 106 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 8 through 24 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 25 through 33 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 34 through 62 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 63 through 89 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 90 through 100 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 101 through 106 )

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