PDB-7krt: Restraining state of a truncated Hsp70 DnaK

ID or keywords:

Entry

Database: PDB / ID: 7krt

Title

Restraining state of a truncated Hsp70 DnaK

Components

Chaperone protein DnaK

Keywords

CHAPERONE /

molecular chaperone /

Hsp70 /

protein folding

Function / homology

Function and homology information

unfolded protein binding /

protein folding /

ATP hydrolysis activity /

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.79 Å

Authors

Wang, W. / Hendrickson, W.A.

Funding support

United States, 1items

Citation

Journal: Mol.Cell / Year: 2021
Title: Conformational equilibria in allosteric control of Hsp70 chaperones.
Authors: Wang, W. / Liu, Q. / Liu, Q. / Hendrickson, W.A.

History

Deposition	Nov 20, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 15, 2021	Provider: repository / Type: Initial release
Revision 1.1	Oct 20, 2021	Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7krt.cif.gz	880.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7krt.ent.gz	728.8 KB	Display	PDB format
PDBx/mmJSON format	7krt.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/kr/7krt ftp://data.pdbj.org/pub/pdb/validation_reports/kr/7krt	HTTPS FTP

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Related structure data

Related structure data	7ko2SC 7kruC 7krvC 7krwC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4b9q-2 4b9q-4 7krt-4 4b9q-3 7ko2-1 7krt-2 4b9q-1 7ko2-3 7ko2-2 5e84-6 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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 - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

7ko2SC

7kruC

7krvC

7krwC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#32 - Aug 2002 Chaperones similarity (10)

Deposited unit

A: Chaperone protein DnaK

B: Chaperone protein DnaK

C: Chaperone protein DnaK

D: Chaperone protein DnaK

hetero molecules

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

1

A: Chaperone protein DnaK

hetero molecules

defined by author&software
Evidence: cross-linking, Intra-chain disulfide bridge was introduced between mutational residue CYS47 and CYS529.
65.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Chaperone protein DnaK

hetero molecules

defined by author&software
65.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Chaperone protein DnaK

hetero molecules

defined by author&software
65.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Chaperone protein DnaK

hetero molecules

defined by author&software
65.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	77.469, 199.529, 94.231
Angle α, β, γ (deg.)	90.000, 93.750, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Chaperone protein DnaK / / HSP70 / Heat shock 70 kDa protein / Heat shock protein 70 Mass: 64996.418 Da / Num. of mol.: 4 / Fragment: Truncated (2-600) / Mutation: E47C, T199A, F529C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: dnaK, FAZ83_07380 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A6D2W465
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.8 Å³/Da / Density % sol: 56 %
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M magnesium acetate, 0.1 M sodium cacodylate pH 6.5, 20% PEG 8000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 14, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 2.79→47.02 Å / Num. obs: 70764 / % possible obs: 99.6 % / Redundancy: 14.2 % / CC_1/2: 0.784 / CC star: 0.938 / R_merge(I) obs: 0.713 / R_pim(I) all: 0.195 / R_rim(I) all: 0.739 / Net I/σ(I): 5.74
Reflection shell	Resolution: 2.79→2.89 Å / Redundancy: 13.6 % / R_merge(I) obs: 3.25 / Num. unique obs: 7064 / CC_1/2: 0.28 / CC star: 0.66 / R_pim(I) all: 0.91 / R_rim(I) all: 3.38 / % possible all: 99.3

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Processing

Software

Name	Version	Classification
Aimless	0.5.32	data scaling
PHENIX	1.18.2_3874	refinement
PDB_EXTRACT	3.27	data extraction
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7KO2

7ko2

Resolution: 2.79→47.02 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 41.36 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.3083	1535	2.18 %
R_work	0.279	63387	-
obs	0.2796	70685	99.83 %

Solvent computation

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

Displacement parameters

B_iso max: 147.94 Å² / B_iso mean: 61.7042 Å² / B_iso min: 6.44 Å²

Refinement step

Cycle: final / Resolution: 2.79→47.02 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17752	0	128	39	17919
B_iso mean	-	-	50.42	41.14	-
Num. residues	-	-	-	-	2396

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	18085
X-RAY DIFFRACTION	f_angle_d	0.694	24528
X-RAY DIFFRACTION	f_dihedral_angle_d	13.492	6740
X-RAY DIFFRACTION	f_chiral_restr	0.046	2909
X-RAY DIFFRACTION	f_plane_restr	0.004	3243

LS refinement shell

Resolution: 2.79→3.338 Å / R_factor R_free error: 0

	R_factor	Num. reflection	% reflection
R_work	0.357	28680	-
R_free	-	632	-
obs	-	-	99.76 %

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	-0.0053	-0.0069	0.0135	-0.0118	0.0193	0.0149	0.0188	-0.133	0.1906	0.0334	0.0488	-0.0433	-0.0817	0.1437	0	-0.1009	0.3252	0.2546	-0.5102	-0.4677	-1.0781	-33.2959	28.9684	-40.0906
2	0.0104	-0.0124	0.0063	0.0029	0.0039	-0.0016	-0.0886	0.0083	-0.12	-0.0249	-0.0172	-0.0213	0.0907	0.0333	0	-0.0578	0.2453	0.1147	-0.2062	-0.1246	0.1361	-35.1445	7.6947	-44.0359
3	0.0149	-0.0046	-0.0297	0.0055	-0.0123	-0.003	0.046	0.0691	0.1078	0.0328	0.0201	0.0441	-0.0476	0.1197	0	0.1226	-0.0291	0.0105	0.0784	0.0109	0.1063	-22.1994	32.6147	-54.2932
4	0.019	-0.0039	0.0176	0.0043	-0.0068	0.0063	-0.0529	-0.0467	-0.1272	0.0349	-0.1059	0.0105	0.1188	0.1458	-0	0.0308	0.1293	0.0987	0.0533	-0.1448	0.3592	-11.9782	3.1725	-46.3492
5	0.0072	-0.0048	-0.0014	-0.0032	0.0028	0.0046	-0.0607	0.1622	0.0221	0.0304	-0.017	0.0793	-0.0755	-0.2608	-0	-0.2736	0.3457	0.1791	0.1898	-0.1145	0.0503	-51.2157	26.1011	-67.0038
6	0.0001	-0.0135	-0.0068	-0.0158	-0.0048	0.0021	-0.0233	-0.008	0.0092	-0.0017	-0.0121	0.1063	0.0051	-0.0214	-0	0.0858	0.3101	0.0963	0.1499	-0.0278	0.2332	-45.8475	13.5979	-32.0119
7	0.0073	0.0044	-0.0023	0.0057	0.0017	0.0052	0.0055	-0.0263	-0.0422	0.0306	-0.0553	-0.0035	0.0686	-0.0349	-0	0.8074	-0.1516	-0.1695	0.9393	0.3108	0.5758	-33.2467	1.0001	-1.0057
8	0.0435	-0.0179	0.0068	0.0087	-0.0027	0.0011	0.0004	0.0034	-0.0053	-0.0142	0.0024	-0.0086	0.0077	0.0004	0	0.1876	0.0306	-0.0031	0.2793	0.0292	0.4892	-21.5174	21.0299	-45.8284
9	-0.0049	-0.0051	-0.0177	0.009	-0.0047	0.0208	-0.0615	0.068	-0.0376	0.0124	0.0867	0.0328	0.0719	0.0887	0	0.1772	0.3692	0.0324	0.1424	-0.6253	0.0285	-34.061	57.3687	-18.3058
10	0.0112	0.0004	-0.004	0.0112	0.0013	0.0005	0.0127	-0.0058	0.0499	0.0013	-0.0275	0.0401	-0.0447	0.043	-0	0.3448	0.1098	-0.0766	0.5305	-0.1344	0.483	-36.6897	78.0561	-12.0025
11	0.0051	-0.0073	-0.0313	0.0203	0.0083	0.007	0.1065	-0.1485	-0.2181	0.0403	0.0136	-0.0309	0.1319	0.0239	0	0.3753	0.4714	-0.092	0.5377	-0.6198	0.3981	-23.0046	52.6814	-4.421
12	0.0123	0.0023	-0.0037	0.0033	-0.0103	0.0075	0.0832	0.1098	0.0426	-0.0182	0.1153	-0.0588	-0.0757	0.0621	0	0.2219	0.0122	0.0433	0.7431	-0.2555	0.4681	-13.4489	82.5734	-9.4147
13	0.0054	-0.017	0.0022	0.0042	0.0039	0.0055	0.1421	-0.0035	0.0092	0.1061	0.1386	0.1157	0.0443	-0.0772	-0	0.5926	0.1438	0.0488	0.5535	-0.073	0.5064	-52.5984	56.7871	8.1681
14	0.0071	-0.0071	0.0077	-0.0012	-0.0072	0.0023	-0.0669	-0.0212	0.0341	-0.0377	-0.06	0.0093	-0.0122	-0.0093	0	0.2341	0.1321	-0.0781	0.4912	-0.0397	0.4488	-47.029	72.5326	-25.1521
15	0.0096	-0.0031	-0.0001	0.0056	-0.0057	0.0055	0.0058	0.0634	-0.0083	-0.1	0.0385	-0.0148	-0.1136	0.0151	0	0.8996	0.3342	-0.0044	0.8275	0.1407	0.7557	-32.772	86.0415	-54.7358
16	0.0315	0.0143	-0.0038	0.0069	-0.0004	0.0009	0.0079	0.0019	0.0039	-0.0011	0.0025	-0.0117	0.0021	0.0105	-0	0.3806	0.005	-0.0368	0.5934	-0.1328	0.5044	-22.7794	64.8201	-11.9289
17	-0.0085	0.0118	0.0325	-0.0065	-0.0071	0.023	-0.0026	-0.057	0.0602	-0.2559	-0.0159	0.0719	-0.0343	0.0061	-0	0.0689	0.0564	-0.0023	-0.2106	0.4176	-0.8202	3.8275	26.0612	-22.7337
18	-0.0087	0.0051	0.01	0.0194	-0.0124	0.0099	0.0032	0.0706	-0.116	-0.0491	-0.0855	0.0098	0.0185	-0.0174	0	0.1956	0.0728	-0.0465	-0.2813	0.2319	-0.0803	6.5394	4.4695	-22.9223
19	-0.0126	0.0228	-0.0328	0.0053	0.026	0.031	0.0277	-0.1591	0.0844	0.082	0.1036	0.0024	-0.1	-0.2027	0	0.0636	0.1391	0.2241	-0.0182	-0.2428	-0.0728	-7.2746	26.571	-8.1926
20	-0.0035	0.0109	-0.004	0.0135	0.0104	0.0112	-0.0286	-0.0958	0.026	0.0502	-0.0382	0.0048	0.0107	-0.0748	-0	0.1865	-0.0252	0.025	0.1893	0.0803	0.3689	-16.1074	-1.4644	-21.5669
21	0.0012	-0.0084	0.0257	0.0106	0.0168	0.0196	0.0985	-0.098	0.0101	0.0907	0.1205	-0.0546	-0.0361	0.1393	-0	0.3609	0.0398	-0.0081	0.1793	0.0061	0.0081	22.7447	19.3526	2.6506
22	-0.004	-0.0071	0.0051	-0.0053	0.0068	-0.0013	-0.0302	0.0155	0.018	-0.0323	0.0104	0.0323	0.0091	0.0144	-0	0.1633	0.0238	0.0407	0.0855	-0.1514	0.1665	16.814	13.8196	-33.9491
23	0.0054	-0.0068	-0.0058	0.0031	0.0039	0.007	-0.0022	0.0063	-0.0688	-0.1354	-0.0087	0.0302	0.0409	0.0311	-0	0.3532	0.1312	-0.0473	0.5131	-0.2826	0.3797	1.937	6.0338	-64.6635
24	0.0274	0.013	0.0069	0.005	0.0026	0.0009	0.0069	-0.0007	0.0018	-0.004	0.0037	0.0007	0.0043	-0.0079	0	0.233	0.035	0.1029	0.2611	-0.0515	0.2136	-7.3814	16.8898	-18.553
25	-0.0047	0.0211	-0.0011	-0.0031	-0.0084	0.0062	0.0653	0.1383	-0.0471	0.0947	0.2191	0.134	0.2019	-0.0093	0	0.1204	-0.3233	0.0018	-0.3152	0.478	0.1182	2.8938	60.1801	-34.6238
26	-0.0074	0.0085	-0.0114	0.0025	-0.0034	-0.0046	0.0641	-0.0998	0.0684	0.0192	0.1076	-0.0286	-0.085	-0.0094	0	0.047	-0.2952	0.1466	-0.4243	0.5154	0.0896	5.1882	81.8959	-33.3328
27	0.0251	0.0254	-0.0195	0.016	0.0111	0.0178	0.0067	0.1357	-0.0048	-0.0879	0.0388	0.0196	0.1093	-0.0351	-0	0.3339	-0.3649	-0.1806	0.4106	0.2526	0.4468	-7.969	60.0313	-49.0652
28	0.0041	-0.0041	0.0109	-0.0012	0.0026	-0.0089	0.0825	-0.0236	0.0022	0.0058	0.1406	0.0778	-0.0987	-0.0215	0	-0.1823	0.4251	-0.1658	0.5568	0.3714	0.5022	-18.1492	86.96	-34.5291
29	0	0.0225	-0.0069	0.0222	0.013	0.0247	-0.0303	0.0508	0.0676	-0.0489	0.0057	0.0086	-0.0169	0.0823	-0	0.3242	-0.0114	-0.0119	0.1574	-0.0202	0.2223	21.6178	68.6174	-59.8439
30	-0.0004	0.0114	0.0038	0.0028	0.0012	0.0026	-0.0454	-0.0232	0.0045	-0.0219	0.0056	0.0048	-0.0113	0.0053	0	0.2611	-0.0107	0.0374	0.1834	-0.043	0.3108	15.7459	72.7147	-23.0077
31	0.0073	-0.0026	0.0008	0.0023	0.0042	0.0066	0.0577	0.0332	-0.0436	0.0502	-0.0065	0.0075	-0.0188	0.025	0	0.3389	0.0184	0.0646	0.4956	-0.0662	0.2942	0.2781	79.0886	9.0078
32	0.0061	-0.0019	-0.0013	0.0015	0.0002	0.0007	0.0067	0.002	-0.004	0.001	0.0049	-0.0013	0.0023	-0.0002	0	0.4696	-0.0614	-0.0672	0.5795	0.0217	0.6072	-8.5056	69.3234	-38.2397

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 ((resid 2 through 39 ) or (resid 116 through 188 ))	A	0
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 40 through 115 )	A	40 - 115
3	X-RAY DIFFRACTION	3	chain 'A' and ((resid 189 through 228 ) or (resid 307 through 393))	A	0
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 229 through 306 )	A	229 - 306
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 394 through 506 )	A	394 - 506
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 507 through 534 )	A	507 - 534
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 535 through 600 )	A	535 - 600
8	X-RAY DIFFRACTION	8	chain A and (resname ATP or (water and within (2.5, element mg)) or element mg)	A	0
9	X-RAY DIFFRACTION	9	chain 'B' and ((resid 2 through 39 ) or (resid 116 through 188 ))	B	0
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 40 through 115 )	B	40 - 115
11	X-RAY DIFFRACTION	11	chain 'B' and ((resid 189 through 228 ) or (resid 307 through 393))	B	0
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 229 through 306 )	B	229 - 306
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 394 through 506 )	B	394 - 506
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 507 through 534 )	B	507 - 534
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 535 through 600 )	B	535 - 600
16	X-RAY DIFFRACTION	16	chain B and (resname ATP or (water and within (2.5, element mg)) or element mg)	B	0
17	X-RAY DIFFRACTION	17	chain 'C' and ((resid 2 through 39 ) or (resid 116 through 188 ))	C	0
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 40 through 115 )	C	40 - 115
19	X-RAY DIFFRACTION	19	chain 'C' and ((resid 189 through 228 ) or (resid 307 through 393))	C	0
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 229 through 306 )	C	229 - 306
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 394 through 506 )	C	394 - 506
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 507 through 534 )	C	507 - 534
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 535 through 600 )	C	535 - 600
24	X-RAY DIFFRACTION	24	chain C and (resname ATP or (water and within (2.5, element mg)) or element mg)	C	0
25	X-RAY DIFFRACTION	25	chain 'D' and ((resid 2 through 39 ) or (resid 116 through 188 ))	D	0
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 40 through 115 )	D	40 - 115
27	X-RAY DIFFRACTION	27	chain 'D' and ((resid 189 through 228 ) or (resid 307 through 393))	D	0
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 229 through 306 )	D	229 - 306
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 394 through 506 )	D	394 - 506
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 507 through 534 )	D	507 - 534
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 535 through 600 )	D	535 - 600
32	X-RAY DIFFRACTION	32	chain D and (resname ATP or (water and within (2.5, element mg)) or element mg)	D	0

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