PDB-4j80: Thermus thermophilus DnaJ

ID or keywords:

Entry

Database: PDB / ID: 4j80

Title

Thermus thermophilus DnaJ

Components

Chaperone protein DnaJ 2

Keywords

CHAPERONE / molecular chaperone / THERMUS THERMOPHILUS DNAJ2 DELTA MUTANT

Function / homology

Function and homology information

chaperone cofactor-dependent protein refolding / unfolded protein binding / protein refolding / DNA replication / cytoplasm
Similarity search - Function

Biological species

Thermus thermophilus (bacteria)

Method

X-RAY DIFFRACTION / EPR /

SYNCHROTRON /

SAD / Resolution: 2.9 Å

Authors

Barends, T.R.M. / Brosi, R.W. / Steinmetz, A. / Scherer, A. / Hartmann, E. / Eschenbach, J. / Lorenz, T. / Seidel, R. / Shoeman, R. / Zimmermann, S. ...

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Combining crystallography and EPR: crystal and solution structures of the multidomain cochaperone DnaJ.
Authors: Barends, T.R. / Brosi, R.W. / Steinmetz, A. / Scherer, A. / Hartmann, E. / Eschenbach, J. / Lorenz, T. / Seidel, R. / Shoeman, R.L. / Zimmermann, S. / Bittl, R. / Schlichting, I. / Reinstein, J.

History

Deposition	Feb 14, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 31, 2013	Provider: repository / Type: Initial release
Revision 1.1	Oct 9, 2013	Group: Database references
Revision 1.2	Oct 16, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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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PDBx/mmCIF format	4j80.cif.gz	431.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4j80.ent.gz	363.5 KB	Display	PDB format
PDBx/mmJSON format	4j80.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4j80_validation.pdf.gz	456.5 KB	Display	wwPDB validaton report
Full document	4j80_full_validation.pdf.gz	468.1 KB	Display
Data in XML	4j80_validation.xml.gz	41.6 KB	Display
Data in CIF	4j80_validation.cif.gz	53 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j8/4j80 ftp://data.pdbj.org/pub/pdb/validation_reports/j8/4j80	HTTPS FTP

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Related structure data

Related structure data	4j7zC C: citing same article (ref.)
Similar structure data	4j80-2 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#32 - Aug 2002 Chaperones similarity (1) #47 - Nov 2003 Simian Virus 40 similarity (4) #80 - Aug 2006 AAA+ Proteases similarity (4)

Deposited unit

A: Chaperone protein DnaJ 2

B: Chaperone protein DnaJ 2

C: Chaperone protein DnaJ 2

D: Chaperone protein DnaJ 2

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

1

A: Chaperone protein DnaJ 2

B: Chaperone protein DnaJ 2

defined by author&software
63.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Chaperone protein DnaJ 2

D: Chaperone protein DnaJ 2

defined by author&software
63.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	102.090, 105.000, 130.030
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Chaperone protein DnaJ 2 Mass: 31816.145 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 2-114 / Mutation: L57(MSE), I142(MSE), L173(MSE), L226(MSE), K231G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: dnaJ2, TTHA1489 / Production host: Escherichia coli (E. coli) / References: UniProt: Q56237
Has protein modification	Y

#1: Protein

Chaperone protein DnaJ 2

Mass: 31816.145 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 2-114 / Mutation: L57(MSE), I142(MSE), L173(MSE), L226(MSE), K231G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: dnaJ2, TTHA1489 / Production host:

Escherichia coli (E. coli) / References: UniProt: Q56237

Has protein modification

Y

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Experiment

Experiment

Method	Number of used crystals
X-RAY DIFFRACTION	1
EPR	1

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Sample preparation

Crystal	Density Matthews: 2.74 Å³/Da / Density % sol: 55.08 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 16% PEG6000, 0.1 M succinate/BTP, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 90 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00767 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 1, 2007
Radiation	Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00767 Å / Relative weight: 1
Reflection	Resolution: 2.8→20 Å / Num. all: 34862 / Num. obs: 34862 / % possible obs: 99.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shell	Resolution: 2.8→2.9 Å / R_merge(I) obs: 0.561 / Mean I/σ(I) obs: 2.7 / % possible all: 99.6

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
SHARP		phasing
REFMAC	5.2.0005	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.9→20 Å / Cor.coef. F_o:F_c: 0.896 / Cor.coef. F_o:F_c free: 0.859 / SU B: 50.613 / SU ML: 0.442 / Cross valid method: THROUGHOUT / ESU R Free: 0.486 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.30739	1591	5.1 %	RANDOM
R_work	0.26489	-	-	-
obs	0.26697	29726	98.88 %	-
all	-	29725	-	-

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: 95.697 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.92 Å²	0 Å²	0 Å²
2-	-	-0.35 Å²	0 Å²
3-	-	-	1.28 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8460	0	0	0	8460

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.022	8680
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	0.893	1.999	11764
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.147	5	1080
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.625	22.5	400
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.816	15	1416
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.627	15	96
X-RAY DIFFRACTION	r_chiral_restr	0.055	0.2	1216
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.022	6836
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1808
X-RAY DIFFRACTION	r_nbd_refined	0.217	0.2	1910
X-RAY DIFFRACTION	r_nbd_other	0.204	0.2	8330
X-RAY DIFFRACTION	r_nbtor_refined	0.185	0.2	4202
X-RAY DIFFRACTION	r_nbtor_other	0.085	0.2	5146
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.132	0.2	178
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.111	0.2	3
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.23	0.2	47
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.315	0.2	189
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.233	0.2	11
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	0.383	1.5	5408
X-RAY DIFFRACTION	r_mcbond_other	0.043	1.5	2184
X-RAY DIFFRACTION	r_mcangle_it	0.701	2	8704
X-RAY DIFFRACTION	r_scbond_it	0.615	3	3272
X-RAY DIFFRACTION	r_scangle_it	0.973	4.5	3060
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.9→2.975 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.392	103	-
R_work	0.334	2181	-
obs	-	-	99.69 %

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	7.5442	-2.1874	0.6749	6.8972	-0.2071	13.3801	-0.0191	-0.0382	-0.5757	-0.5252	-0.0744	-0.1633	0.7329	0.2119	0.0935	0.3165	0.0601	-0.0184	0.1337	-0.0862	0.2351	-1.9874	19.1379	89.0911
2	16.4604	-4.5011	8.088	15.3628	-0.8367	8.2533	0.0811	-0.6784	-0.6027	0.2348	-0.1974	0.3808	0.1404	-0.2983	0.1163	0.2019	-0.0217	-0.0565	0.2288	-0.0714	0.2364	-16.8268	21.0269	91.0943
3	1.5942	-3.3308	0.1773	13.7428	-2.5629	0.7466	0.0171	-0.4681	-0.1502	0.9075	-0.1098	-0.1545	-0.3693	0.2992	0.0927	0.4902	-0.0747	-0.0916	0.4363	0.0979	0.2977	-28.5133	49.4279	78.2771
4	15.8398	-12.5717	-0.0295	17.7573	-0.7181	1.6612	-0.2002	-0.4331	2.3584	0.5369	0.4164	0.2375	-0.4729	0.6087	-0.2162	0.4798	-0.2518	-0.0694	0.2774	0.0083	1.1105	-42.1185	79.2037	65.4749
5	13.0846	0.4996	-1.4876	17.7622	7.8133	23.5393	0.6542	0.3661	1.202	-0.4833	-0.3459	2.4885	-0.2914	-3.8129	-0.3083	0.5651	-0.0206	-0.3482	1.976	0.5823	1.5463	-101.0555	25.5357	37.6356
6	34.9584	4.1463	6.7598	16.2626	3.8936	13.8004	0.3898	0.0942	-1.7389	-0.5838	1.3614	1.2924	2.5103	-2.9365	-1.7512	0.8979	-0.5621	-0.37	1.0945	0.6607	0.7142	-88.5085	18.1449	41.5087
7	2.437	3.3169	1.4439	13.5401	6.1672	3.017	0.0508	0.5035	0.3597	-0.722	-0.1525	0.861	-0.3737	-0.1421	0.1016	0.3313	0.041	0.0627	0.3344	0.1079	0.4071	-74.7203	47.1326	50.6102
8	11.4545	11.8685	0.6465	16.1918	0.7234	1.6395	-0.434	0.2134	2.2174	-0.41	0.2724	0.5002	-0.4832	-0.3705	0.1616	0.3994	0.1162	-0.0289	0.0996	0.0003	1.3041	-62.9032	77.9722	63.3012
9	7.4571	-0.8905	-0.3183	11.1548	0.6492	10.2235	0.174	-0.4035	-0.4588	0.4887	-0.046	0.5283	1.191	-0.7778	-0.128	0.5144	-0.1993	0.0181	0.4423	0.0594	0.269	-18.8337	59.3758	102.9353
10	9.2709	-3.6647	-0.3412	14.4077	8.8181	5.873	0.1345	0.337	0.3223	-0.0187	-0.5234	0.5846	0.0349	-0.4267	0.3889	0.2488	-0.0174	0.0351	0.6255	0.1918	0.3712	-16.6591	73.9082	101.8667
11	21.0539	-3.3184	-10.9015	0.6325	1.4393	6.8423	-0.4182	1.7009	-0.9121	-0.1006	-0.2695	0.0027	0.3635	-0.968	0.6877	0.6173	0.1175	0.122	0.6435	-0.2021	0.3736	-42.6391	82.7667	115.9735
12	20.5874	-9.7729	-0.4053	8.6733	-0.5846	3.4067	0.3161	1.1925	-1.1745	-0.3738	-0.2933	2.0932	0.5913	-0.7127	-0.0227	0.2244	-0.0978	-0.0901	0.4732	-0.1332	0.7635	-74.6543	90.252	128.7797
13	18.7087	9.0087	6.2209	18.8965	0.3837	20.1086	-1.0794	-1.9298	3.7729	2.3252	-0.544	-1.429	-2.3193	1.0093	1.6235	1.8188	-0.5638	-0.418	1.1419	-0.2804	2.1256	-15.7763	157.0451	156.1243
14	17.7036	1.5103	-3.7508	21.027	1.1117	20.9982	0.3441	-1.7591	1.0337	1.0802	0.0417	0.4967	-2.0237	-0.4128	-0.3858	0.7002	-0.3361	0.2251	0.8576	-0.152	0.5703	-27.2424	147.2745	154.4942
15	9.1559	2.8067	3.9094	2.7559	1.5111	4.0368	0.0995	0.0003	0.6861	0.1842	-0.1464	0.0429	-0.4096	-0.2749	0.0469	0.3015	0.1176	0.0183	0.215	-0.0084	0.1541	-51.7124	128.2129	143.8933
16	15.0805	11.9888	3.1261	15.4654	2.1893	2.198	0.2465	-0.0474	0.0184	0.2914	-0.1134	1.8889	-0.1365	-0.7563	-0.1332	0.199	0.1718	-0.034	0.5171	0.0506	0.6919	-78.8847	110.4228	130.1346

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 70
2	X-RAY DIFFRACTION	2	A	71 - 107
3	X-RAY DIFFRACTION	3	A	108 - 176
4	X-RAY DIFFRACTION	4	A	177 - 265
5	X-RAY DIFFRACTION	5	B	2 - 70
6	X-RAY DIFFRACTION	6	B	71 - 107
7	X-RAY DIFFRACTION	7	B	108 - 176
8	X-RAY DIFFRACTION	8	B	177 - 265
9	X-RAY DIFFRACTION	9	C	2 - 70
10	X-RAY DIFFRACTION	10	C	71 - 107
11	X-RAY DIFFRACTION	11	C	108 - 176
12	X-RAY DIFFRACTION	12	C	177 - 265
13	X-RAY DIFFRACTION	13	D	2 - 70
14	X-RAY DIFFRACTION	14	D	71 - 107
15	X-RAY DIFFRACTION	15	D	108 - 176
16	X-RAY DIFFRACTION	16	D	177 - 265

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