PDB-4eld: Crystal Structure of an Activated Variant of Small Heat Shock Pro...

ID or keywords:

Entry

Database: PDB / ID: 4eld

Title

Crystal Structure of an Activated Variant of Small Heat Shock Protein Hsp16.5

Components

Small heat shock protein HSP16.5

Keywords

CHAPERONE

Function / homology

Function and homology information

protein complex oligomerization / response to salt stress / protein folding chaperone / response to hydrogen peroxide / unfolded protein binding / protein folding / response to heat / protein stabilization / protein-containing complex / identical protein binding / cytoplasm
Similarity search - Function

Biological species

Methanocaldococcus jannaschii (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.701 Å

Authors

Spiller, B.W. / Mchaourab, H.S. / Lin, Y.-L.

Citation

Journal: Biochemistry / Year: 2012
Title: Crystal structure of an activated variant of small heat shock protein hsp16.5.
Authors: McHaourab, H.S. / Lin, Y.L. / Spiller, B.W.

History

Deposition	Apr 10, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 13, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jun 20, 2012	Group: Database references
Revision 1.2	Jul 11, 2012	Group: Database references
Revision 1.3	Sep 13, 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 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4eld.cif.gz	107.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4eld.ent.gz	84.8 KB	Display	PDB format
PDBx/mmJSON format	4eld.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4eld_validation.pdf.gz	439.8 KB	Display	wwPDB validaton report
Full document	4eld_full_validation.pdf.gz	442.6 KB	Display
Data in XML	4eld_validation.xml.gz	9.9 KB	Display
Data in CIF	4eld_validation.cif.gz	12.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/el/4eld ftp://data.pdbj.org/pub/pdb/validation_reports/el/4eld	HTTPS FTP

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Related structure data

Related structure data	1shsS S: Starting model for refinement
Similar structure data	6ipo-1 5cw0-1 10097 6jja-1 5042 Search similar-shape structures by Omokage search (details) 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 HSP16.5

B: Small heat shock protein HSP16.5

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

1

A: Small heat shock protein HSP16.5

B: Small heat shock protein HSP16.5

x 24

defined by software
852 kDa, 48 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_555	-x,-y,z	1
crystal symmetry operation	3_555	-x,y,-z	1
crystal symmetry operation	4_555	x,-y,-z	1
crystal symmetry operation	5_555	z,x,y	1
crystal symmetry operation	6_555	z,-x,-y	1
crystal symmetry operation	7_555	-z,-x,y	1
crystal symmetry operation	8_555	-z,x,-y	1
crystal symmetry operation	9_555	y,z,x	1
crystal symmetry operation	10_555	-y,z,-x	1
crystal symmetry operation	11_555	y,-z,-x	1
crystal symmetry operation	12_555	-y,-z,x	1
crystal symmetry operation	13_555	y,x,-z	1
crystal symmetry operation	14_555	-y,-x,-z	1
crystal symmetry operation	15_555	y,-x,z	1
crystal symmetry operation	16_555	-y,x,z	1
crystal symmetry operation	17_555	x,z,-y	1
crystal symmetry operation	18_555	-x,z,y	1
crystal symmetry operation	19_555	-x,-z,-y	1
crystal symmetry operation	20_555	x,-z,y	1
crystal symmetry operation	21_555	z,y,-x	1
crystal symmetry operation	22_555	z,-y,x	1
crystal symmetry operation	23_555	-z,y,x	1
crystal symmetry operation	24_555	-z,-y,-x	1

Unit cell

Length a, b, c (Å)	184.583, 184.583, 184.583
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	211
Space group name H-M	I432

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details	Auth asym-ID	Auth seq-ID
1	1	1	chain 'A' and (resseq 48:149 ) and (not element H) and (not element D)	A	0
2	1	1	chain 'B' and (resseq 48:149 ) and (not element H) and (not element D)	B	0

#1: Protein	Small heat shock protein HSP16.5 / MJ16.5-P1 Mass: 17755.477 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 Gene: MJ0285 / Plasmid: pET20b-derived / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q57733
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Small heat shock protein HSP16.5 / MJ16.5-P1

Mass: 17755.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Methanocaldococcus jannaschii (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: MJ0285 / Plasmid: pET20b-derived / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q57733

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.69 Å³/Da / Density % sol: 66.66 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.8 M ammonium sulfate, 20 mM Tris, pH 8.0, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97945 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 30, 2006
Radiation	Monochromator: Rosenbaum-Rock double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97945 Å / Relative weight: 1
Reflection	Resolution: 2.7→50 Å / Num. all: 15068 / Num. obs: 14902 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.7 % / B_iso Wilson estimate: 80 Å² / R_merge(I) obs: 0.043 / Net I/σ(I): 29.6
Reflection shell	Resolution: 2.7→2.9 Å / Redundancy: 4.7 % / R_merge(I) obs: 0.6 / Mean I/σ(I) obs: 2.1 / R_sym value: 0.6 / % possible all: 100

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Processing

Software

Name	Classification
SERGUI	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SHS

1shs

Resolution: 2.701→49.332 Å / SU ML: 0.75 / σ(F): 1.34 / Phase error: 24.82 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2367	1491	10.01 %	RANDOM, THROUGHOUT
R_work	0.2138	-	-	-
obs	0.2161	14902	98.92 %	-
all	-	15068	-	-

Solvent computation

Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 67.621 Å² / k_sol: 0.362 e/Å³

Refine analyze

Luzzati sigma a obs: 0.75 Å

Refinement step

Cycle: LAST / Resolution: 2.701→49.332 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1791	0	0	10	1801

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	1815
X-RAY DIFFRACTION	f_angle_d	1.089	2450
X-RAY DIFFRACTION	f_dihedral_angle_d	16.865	708
X-RAY DIFFRACTION	f_chiral_restr	0.075	290
X-RAY DIFFRACTION	f_plane_restr	0.004	313

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	797	X-RAY DIFFRACTION	POSITIONAL	0.1
1	2	B	797	X-RAY DIFFRACTION	POSITIONAL	0.1

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 (%)
2.701-2.7882	0.3734	134	0.3556	1204	X-RAY DIFFRACTION	100
2.7882-2.8879	0.347	135	0.3331	1216	X-RAY DIFFRACTION	100
2.8879-3.0035	0.3395	133	0.3031	1198	X-RAY DIFFRACTION	100
3.0035-3.1402	0.3475	134	0.2708	1209	X-RAY DIFFRACTION	100
3.1402-3.3057	0.2583	135	0.2607	1206	X-RAY DIFFRACTION	100
3.3057-3.5127	0.2781	134	0.2367	1209	X-RAY DIFFRACTION	100
3.5127-3.7839	0.253	135	0.2222	1218	X-RAY DIFFRACTION	99
3.7839-4.1645	0.2172	136	0.2113	1219	X-RAY DIFFRACTION	99
4.1645-4.7667	0.1769	135	0.162	1223	X-RAY DIFFRACTION	99
4.7667-6.0038	0.22	139	0.1758	1244	X-RAY DIFFRACTION	98
6.0038-49.3401	0.2229	141	0.2124	1265	X-RAY DIFFRACTION	94

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	1.1395	-0.0361	0.0772	1.5882	1.4442	1.3222	-0.7819	1.9296	-1.0988	-4.6219	0.7176	-1.1305	-0.9588	0.3698	0.042	0.9873	0.0249	0.1092	1.1325	-0.4164	1.1492	-35.3334	14.5398	49.9878
2	4.1516	0.972	-0.9788	1.8209	-0.6548	3.8365	0.0211	-0.2672	-0.3309	-0.3499	-0.0191	0.1685	0.1721	-0.28	-0.0016	0.5574	0.0246	-0.0123	0.4952	-0.0515	0.7179	-38.3256	17.5651	59.5583
3	0.414	4.0068	0.2017	2.3614	-0.8924	1.6047	-0.7107	1.1282	0.2852	-0.6046	0.7505	0.6377	-0.0216	-0.4177	-0.003	0.7778	-0.0697	-0.05	0.8735	0.0433	1.0256	-32.3138	34.8373	50.8022
4	2.2721	-2.3172	-0.2225	2.0175	0.2681	6.6366	0.1623	-0.3163	-0.5904	0.1658	-0.4986	-0.3217	0.6811	-0.3308	-0.0016	0.7035	-0.0121	-0.0022	0.5461	-0.0455	0.6966	-40.1386	11.8179	64.4365
5	0.7415	-0.2956	0.3934	0.5017	0.097	0.4044	-0.1912	-0.4024	-0.5601	2.086	0.3219	-1.8056	0.0747	-0.45	0.001	0.8088	0.1635	-0.0837	0.7995	0.0169	0.8854	-39.1679	-13.0901	67.6174
6	0.1828	-0.134	-0.6104	0.0254	0.0344	0.5221	0.4869	-0.6362	0.2867	-0.5984	-0.4494	-0.1419	-0.3029	1.3752	0.0004	0.77	0.0274	0.2461	0.9247	-0.1638	1.3755	-15.1426	31.232	50.6955
7	1.173	0.5338	1.3405	1.3737	1.3134	2.0607	-0.0222	0.0214	-0.1677	-0.8269	-0.0534	-0.4617	0.2179	-0.0886	-0	0.5529	0.0826	-0.0934	0.6574	-0.0305	0.7079	-22.1225	39.0132	56.5058
8	0.7951	-0.7447	0.5317	1.3644	1.3711	2.7468	-0.3739	-0.1982	-0.0095	0.3755	-0.3186	-2.1484	1.0099	1.2091	-0.062	0.6188	0.0883	-0.1401	0.9525	0.1021	1.4992	-13.1748	33.4405	62.5892
9	0.1263	0.1467	-0.3637	0.3353	-0.3917	1.432	1.8449	-1.6454	-0.1926	2.0123	-1.6039	-0.482	-0.0721	2.6233	0.0512	0.7244	0.0269	-0.151	0.7696	0.2716	1.3013	-24.6094	10.2272	65.1234
10	1.9494	-0.4002	0.0723	0.2541	-0.1154	1.8686	-0.9088	0.7873	-1.9561	-0.1731	-0.1419	-2.5759	0.3053	0.2084	0.0004	1.0244	0.0197	0.0851	0.7477	-0.0218	1.412	-25.1199	12.3781	55.884
11	0.6263	0.9594	1.0381	1.4274	1.2746	1.4144	-0.178	-1.0488	-1.2251	-2.2988	0.1958	-3.4579	0.4715	0.6393	0.0706	0.6482	0.2355	0.4168	0.8885	0.1194	1.9121	-12.3177	30.5169	55.0393
12	0.6726	0.4251	-0.0135	0.8968	-0.7064	0.6165	-0.3019	1.2106	0.2726	0.7213	-0.5303	0.1988	-1.6313	-1.6815	-0.0135	0.6229	-0.1375	-0.1355	0.8794	0.0688	0.8832	-12.1839	47.165	60.2129
13	2.492	-1.884	-0.2514	2.2824	1.9118	3.6951	0.2211	-0.7741	0.023	0.4753	-0.9303	0.4009	-0.201	0.4857	-0.0026	0.4668	-0.0278	-0.0889	0.7174	-0.073	0.8381	-20.5718	42.2136	61.2903
14	1.1526	1.0053	-0.4009	0.4795	-0.4482	0.3116	-0.6767	0.0381	0.5722	1.6047	-0.0687	-1.135	-2.1393	0.1473	0.0041	0.7632	0.1149	-0.0405	0.8417	0.068	0.8195	-18.4196	64.058	46.4702

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 45:58)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 59:96)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 97:124)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 125:153)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 154:161)
6	X-RAY DIFFRACTION	6	chain 'B' and (resseq 48:58)
7	X-RAY DIFFRACTION	7	chain 'B' and (resseq 59:78)
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 79:96)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 97:106)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 107:117)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 118:124)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 125:134)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 135:153)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 154:161)

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