PDB-3vql: Small heat shock protein hsp14.0 of C-terminal deletion variant

ID or keywords:

Entry

Database: PDB / ID: 3vql

Title

Small heat shock protein hsp14.0 of C-terminal deletion variant

Components

Small heat shock protein StHsp14.0

Keywords

CHAPERONE / alpha-crystallin domain

Function / homology

Function and homology information

response to salt stress / response to hydrogen peroxide / : / unfolded protein binding / protein folding / protein complex oligomerization / response to heat
Similarity search - Function

Biological species

Sulfolobus tokodaii (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Hanazono, Y. / Takeda, K. / Miki, K.

Citation

Journal: J.Mol.Biol. / Year: 2012
Title: Structural studies on the oligomeric transition of a small heat shock protein, StHsp14.0
Authors: Hanazono, Y. / Takeda, K. / Yohda, M. / Miki, K.

History

Deposition	Mar 26, 2012	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 6, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jul 24, 2013	Group: Database references
Revision 1.2	Nov 8, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3vql.cif.gz	103.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3vql.ent.gz	81.2 KB	Display	PDB format
PDBx/mmJSON format	3vql.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3vql_validation.pdf.gz	436.4 KB	Display	wwPDB validaton report
Full document	3vql_full_validation.pdf.gz	442.9 KB	Display
Data in XML	3vql_validation.xml.gz	11.7 KB	Display
Data in CIF	3vql_validation.cif.gz	15.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vq/3vql ftp://data.pdbj.org/pub/pdb/validation_reports/vq/3vql	HTTPS FTP

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Related structure data

Related structure data	3vqkC 3vqmC 3aabS 3aac S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3vqm-6 5t1x-3 3vqm-4 5t20-6 5t1x-4 3vqm-3 6grf-2 5t1x-2 1qwi-1 3mpk-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) #127 - Jul 2010 Crystallins similarity (4) #108 - Dec 2008 Hsp90 similarity (1)

Deposited unit

A: Small heat shock protein StHsp14.0

B: Small heat shock protein StHsp14.0

26.5 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)	45.071, 56.935, 78.853
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Small heat shock protein StHsp14.0 Mass: 13235.255 Da / Num. of mol.: 2 / Mutation: deletion of 8 C-terminal residues Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: 7 / Gene: hsp14.0, ST1653 / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q970D9
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	DELETION OF EIGHT C-TERMINAL RESIDUES

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.91 Å³/Da / Density % sol: 35.64 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 50 mM ammonium sulfate, 2.0% PEG8000, 15% glycerol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Oct 30, 2010 / Details: mirrors
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8 Å / Relative weight: 1
Reflection	Resolution: 1.9→50 Å / Num. obs: 16367 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / R_sym value: 0.06 / Net I/σ(I): 25.9
Reflection shell	Resolution: 1.9→1.93 Å / Redundancy: 4 % / Mean I/σ(I) obs: 4 / Num. unique all: 775 / R_sym value: 0.261 / % possible all: 95.9

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
CNS		refinement
PHENIX	(phenix.refine: 1.7.3_928)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
CNS		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AAB

3aab

Resolution: 1.9→28.468 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8436 / SU ML: 0.25 / σ(F): 0 / Phase error: 22.34 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2498	818	5 %	RANDOM
R_work	0.2022	-	-	-
obs	0.2045	16345	98.65 %	-

Solvent computation

Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 56.444 Å² / k_sol: 0.386 e/Å³

Displacement parameters

B_iso max: 129.74 Å² / B_iso mean: 45.8563 Å² / B_iso min: 15.18 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.6309 Å²	-0 Å²	0 Å²
2-	-	-6.6834 Å²	0 Å²
3-	-	-	5.0525 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→28.468 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1752	0	0	88	1840

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	1782
X-RAY DIFFRACTION	f_angle_d	1.324	2407
X-RAY DIFFRACTION	f_chiral_restr	0.09	266
X-RAY DIFFRACTION	f_plane_restr	0.005	313
X-RAY DIFFRACTION	f_dihedral_angle_d	14.968	697

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.9001-2.0191	0.2816	135	0.2497	2489	2624	97
2.0191-2.1749	0.2355	152	0.2125	2517	2669	98
2.1749-2.3937	0.2356	127	0.1957	2570	2697	99
2.3937-2.7398	0.282	113	0.2092	2600	2713	99
2.7398-3.4509	0.2632	151	0.2066	2616	2767	99
3.4509-28.4707	0.2348	140	0.1906	2735	2875	99

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	1.2291	0.7972	-1.1397	0.4914	-0.7317	0.9528	0.9106	0.033	0.9494	-0.9155	0.9772	-0.1428	-1.9043	0.3323	-0.288	0.9842	-0.1996	-0.0595	0.5355	0.1483	0.7418	10.4141	25.693	-4.0308
2	1.2816	-1.8011	0.7918	3.4205	-1.5665	0.4438	0.2323	0.1173	0.16	-0.0999	0.0151	0.3378	-0.0194	-0.0678	-0.1517	0.2459	0.0247	-0.0747	0.2911	0.0597	0.2591	6.4042	14.777	2.5316
3	0.5516	-0.7875	0.6262	5.5409	1.0271	1.36	-0.1404	-0.1746	-0.388	0.6203	0.2542	0.312	0.3355	-0.0064	-0.0784	0.2135	0.0161	0.0196	0.2116	0.0786	0.3015	10.7225	0.8071	11.7111
4	3.9458	-0.1938	-0.0854	3.5413	-0.5236	2.5883	0.0091	-0.2833	0.1426	0.3436	0.3925	0.9421	0.072	-0.3941	-0.3222	0.1813	0.0035	0.0486	0.3239	0.1556	0.4006	-0.7586	7.3463	10.8607
5	3.752	-0.9674	-5.0754	0.3066	1.3412	7.3452	-0.5598	0.4617	0.6185	1.4159	-0.0453	1.1189	0.4727	-0.3937	-0.0174	0.4511	0.134	0.1033	0.4752	0.1229	0.8844	5.4365	33.9621	7.7963
6	1.6201	1.0788	0.7787	3.3895	0.3649	0.7273	-0.1023	-0.1143	0.1088	-0.3365	0.1456	0.4569	0.0747	-0.2289	-0.0556	0.2492	0.0053	-0.0895	0.2557	0.0697	0.2923	3.5599	13.0654	4.8507
7	0.8127	1.1289	1.3507	3.2623	1.0916	2.3606	-0.8187	-0.1491	-0.8534	0.937	-0.254	1.1669	0.4546	-0.284	0.1771	0.5761	-0.0021	-0.0237	0.3888	0.019	1.0454	2.1809	-10.3547	7.8778
8	4.3955	4.6816	0.1874	2.0706	0.827	2.7834	0.2049	-0.3372	-0.9647	1.0089	0.1252	-0.4283	0.3763	-0.1802	-0.2111	0.3845	-0.0047	-0.0238	0.408	0.1323	0.3622	8.4549	4.7299	18.8257
9	2.1894	3.0874	0.7621	2.0699	3.1225	3.1458	-0.2027	-0.3521	-0.7437	0.915	0.2147	-0.1907	0.872	0.0588	0.0768	0.3499	0.02	0.0106	0.3194	0.1737	0.401	7.9381	-3.995	14.0805
10	2.0661	3.3314	4.1185	1.8582	4.1808	2.059	1.2951	0.693	0.9914	0.2783	1.2637	-0.2644	-0.4417	-0.5841	-0.1571	0.6662	-0.1628	-0.1895	0.5993	-0.1144	0.3488	10.7017	9.3985	-9.1511
11	3.9871	-1.5769	-0.2759	3.6415	-0.4649	2.2318	0.0995	0.3491	-0.2086	-0.1825	0.0265	-0.2581	0.4325	-0.012	-0.1114	0.2678	0.0272	0.0302	0.2904	-0.0162	0.2033	15.7385	10.3747	0.4264
12	3.3874	0.3695	-0.5533	5.2102	-1.5237	3.1208	0.1209	-0.0298	0.5113	1.0115	0.1249	0.1318	-0.6994	-0.1794	-0.2479	0.3513	0.0361	0.0343	0.2194	0.0095	0.2463	12.5368	26.6457	12.9166
13	3.3266	0.4962	0.423	4.4625	1.0382	2.4793	0.0894	-0.2502	-0.282	0.3548	0.2113	-1.2976	-0.1106	0.4426	-0.314	0.1732	-0.0076	-0.0769	0.2474	-0.0253	0.4328	23.7342	20.0607	11.2919
14	3.0952	2.9253	0.5653	4.7306	2.4596	1.613	0.0308	-0.0472	-0.7794	0.2101	0.2594	-1.0527	0.3482	0.1103	-0.2453	0.2422	0.0376	0.0383	0.2281	0.0398	0.465	17.4216	0.6764	5.5487
15	2.8194	0.8116	0.0572	5.8225	0.0343	3.1589	-0.2271	-0.1965	0.8953	0.2623	-0.1858	-1.2062	-0.6448	-0.1157	0.3018	0.3654	0.0327	-0.1513	0.2293	-0.0402	0.4006	21.1929	31.0142	7.9425
16	0.9033	1.5812	-0.3156	2.1558	-2.3233	0.5417	0.0049	-0.2847	0.3049	1.3643	-0.0832	0.0379	-0.6134	-0.3355	0.2788	0.5653	0.0421	-0.0541	0.2868	-0.0279	0.228	15.0885	26.8677	17.36

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain A and (resseq 10:16)	A	10 - 16
2	X-RAY DIFFRACTION	2	chain A and (resseq 17:26)	A	17 - 26
3	X-RAY DIFFRACTION	3	chain A and (resseq 27:46)	A	27 - 46
4	X-RAY DIFFRACTION	4	chain A and (resseq 47:70)	A	47 - 70
5	X-RAY DIFFRACTION	5	chain A and (resseq 71:75)	A	71 - 75
6	X-RAY DIFFRACTION	6	chain A and (resseq 76:88)	A	76 - 88
7	X-RAY DIFFRACTION	7	chain A and (resseq 89:98)	A	89 - 98
8	X-RAY DIFFRACTION	8	chain A and (resseq 99:106)	A	99 - 106
9	X-RAY DIFFRACTION	9	chain A and (resseq 107:115)	A	107 - 115
10	X-RAY DIFFRACTION	10	chain B and (resseq 3:11)	B	3 - 11
11	X-RAY DIFFRACTION	11	chain B and (resseq 12:26)	B	12 - 26
12	X-RAY DIFFRACTION	12	chain B and (resseq 27:46)	B	27 - 46
13	X-RAY DIFFRACTION	13	chain B and (resseq 47:70)	B	47 - 70
14	X-RAY DIFFRACTION	14	chain B and (resseq 71:81)	B	71 - 81
15	X-RAY DIFFRACTION	15	chain B and (resseq 82:98)	B	82 - 98
16	X-RAY DIFFRACTION	16	chain B and (resseq 99:115)	B	99 - 115

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