PDB-3qnj: Crystal structure of the substrate binding domain of E.coli DnaK ...

ID or keywords:

Entry

Database: PDB / ID: 3qnj

Title

Crystal structure of the substrate binding domain of E.coli DnaK in complex with the antimicrobial peptide oncocin

Components

Chaperone protein DnaK
antimicrobial peptide oncocin

Keywords

CHAPERONE/ANTIMICROBIAL PROTEIN / peptide/protein binding / CHAPERONE-ANTIMICROBIAL PROTEIN complex

Function / homology

Function and homology information

stress response to copper ion / sigma factor antagonist activity / chaperone cofactor-dependent protein refolding / protein unfolding / cellular response to unfolded protein / protein folding chaperone /

inclusion body /

heat shock protein binding /

ADP binding / ATP-dependent protein folding chaperone ...
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Oncopeltus fasciatus (milkweed bug)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.28 Å

Authors

Zahn, M. / Straeter, N.

Citation

Journal: Chembiochem / Year: 2011
Title: Rational Design of Oncocin Derivatives with Superior Protease Stabilities and Antibacterial Activities Based on the High-Resolution Structure of the Oncocin-DnaK Complex.
Authors: Knappe, D. / Zahn, M. / Sauer, U. / Schiffer, G. / Strater, N. / Hoffmann, R.

History

Deposition	Feb 8, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 23, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 8, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Feb 21, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3qnj.cif.gz	184.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3qnj.ent.gz	151.1 KB	Display	PDB format
PDBx/mmJSON format	3qnj.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/qn/3qnj ftp://data.pdbj.org/pub/pdb/validation_reports/qn/3qnj	HTTPS FTP

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Related structure data

Related structure data	1dkx 1dky 1dkz 3dpo 3dpp 3dpq
Similar structure data	4hyb-2 4ezo-2 3dpp-1 4ezw-3 4e81-1 4ezo-1 3dpq-1 4jwc-1 4hy9-2 4hyb-1 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

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: antimicrobial peptide oncocin

D: antimicrobial peptide oncocin

hetero molecules

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

1

A: Chaperone protein DnaK

C: antimicrobial peptide oncocin

hetero molecules

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

2

B: Chaperone protein DnaK

D: antimicrobial peptide oncocin

hetero molecules

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

3

B: Chaperone protein DnaK

D: antimicrobial peptide oncocin

hetero molecules

A: Chaperone protein DnaK

C: antimicrobial peptide oncocin

hetero molecules

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

Unit cell

Length a, b, c (Å)	77.664, 161.137, 44.629
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 DnaK / / HSP70 / Heat shock 70 kDa protein / Heat shock protein 70 Mass: 23820.777 Da / Num. of mol.: 2 / Fragment: UNP residues 389-607 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: dnaK, groP, grpF, seg / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: P0A6Y8
#2: Protein/peptide	antimicrobial peptide oncocin Mass: 2310.741 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: This sequence is derived from oncopeltus fasciatus and optimized for the treatment of Gram-negative pathogens Source: (synth.) Oncopeltus fasciatus (milkweed bug)
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.67 Å³/Da / Density % sol: 53.96 %
Crystal grow	Temperature: 292 K / pH: 4 Details: 2.4 M ammonium sulfate, 0.1 M citric acid, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.8943
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 23, 2010
Radiation	Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8943 Å / Relative weight: 1
Reflection	Resolution: 2.25→25 Å / Num. obs: 25775 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / B_iso Wilson estimate: 35.5 Å² / R_merge(I) obs: 0.071 / Net I/σ(I): 17.7

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Processing

Software

Name	Version	Classification
MAR345		data collection
MOLREP		phasing
REFMAC	5.5.0109	refinement
XDS		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.28→25 Å / Cor.coef. F_o:F_c: 0.93 / Cor.coef. F_o:F_c free: 0.868 / SU B: 15.333 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.284	1010	3.9 %	RANDOM
R_work	0.211	-	-	-
obs	0.213	24726	97.6 %	-

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: 35.289 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.91 Å²	0 Å²	0 Å²
2-	-	-0.11 Å²	0 Å²
3-	-	-	3.02 Å²

Refinement step

Cycle: LAST / Resolution: 2.28→25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3307	0	30	148	3485

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.022	3477
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.855	1.987	4714
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.445	5	453
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.687	26.139	158
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.59	15	660
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.945	15	19
X-RAY DIFFRACTION	r_chiral_restr	0.122	0.2	547
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	2573
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	0.771	1.5	2208
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.362	2	3576
X-RAY DIFFRACTION	r_scbond_it	2.678	3	1269
X-RAY DIFFRACTION	r_scangle_it	4.288	4.5	1129
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.28→2.34 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.327	76	-
R_work	0.245	1713	-
obs	-	-	93.52 %

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	0.8745	-0.6392	1.6663	0.7821	-1.0452	4.1299	-0.066	-0.1384	0.0735	0.0001	0.0135	-0.0235	0.0026	-0.1673	0.0525	0.0715	0.0264	-0.0038	0.0951	-0.0481	0.0463	11.2728	-31.7698	6.486
2	20.2211	-0.6912	20.6181	0.6843	-0.599	26.0498	-0.0569	-0.5172	-0.7492	0.0343	0.4774	0.0476	-1.3574	-0.5098	-0.4205	0.3628	0.0221	-0.0167	0.3354	-0.0122	0.2301	-1.2655	-36.5213	0.2003
3	1.6039	0.2089	1.8091	0.7245	0.2569	2.1097	0.0138	0.1308	-0.0552	-0.0564	0.0467	-0.1194	0.0106	0.0665	-0.0606	0.0534	0.0082	0.0323	0.1132	-0.0257	0.0892	7.2892	-31.467	-7.2425
4	1.0207	0.7418	0.6125	1.649	-0.0053	0.6135	0.1456	-0.1217	-0.2334	-0.0214	-0.0016	0.0441	0.1255	-0.1271	-0.144	0.1352	-0.0287	-0.0245	0.1463	-0.0039	0.2239	-2.9856	-41.0725	-8.0513
5	8.0825	0.8109	1.6301	0.1792	0.2506	0.6038	0.0695	-0.3269	-0.6323	0.0126	0.0246	-0.1335	0.0978	-0.0813	-0.094	0.0953	-0.024	0.0202	0.0935	-0.0265	0.159	5.7119	-44.3153	2.2122
6	5.9612	1.6915	2.3634	0.6987	0.9617	1.4011	0.0619	-0.0645	-0.2761	-0.0671	0.0007	-0.105	-0.0275	-0.0065	-0.0627	0.1292	0.0203	0.0168	0.0848	-0.0384	0.1641	17.8818	-38.8261	-0.2486
7	0.3098	-0.6181	1.0749	5.0718	-0.4199	4.799	-0.2115	-0.0713	0.0802	0.3032	0.2199	-0.3681	-0.654	-0.0256	-0.0084	0.2616	0.0453	-0.0825	0.2263	-0.1016	0.2286	15.5671	-18.3644	0.9535
8	17.5404	1.5113	0.6102	3.5138	-2.3587	2.0704	-0.0016	0.5064	-0.022	-0.0713	-0.031	0.2976	0.2011	0.0399	0.0326	0.1701	0.04	0.044	0.0754	-0.0495	0.2539	-5.4482	-21.7945	-11.6636
9	4.9851	-5.3617	6.5542	6.9183	-6.0805	9.5268	0.8059	-0.1969	-0.7347	-0.8053	0.2416	1.0803	1.2955	-0.1588	-1.0475	0.5359	0.0579	-0.4748	0.9491	-0.1303	1.1185	-21.4265	-20.7444	-24.8967
10	20.0024	-1.3447	3.2778	6.2714	-2.4776	5.5488	-0.2328	1.7272	-0.553	-0.4417	0.1287	0.6178	-0.1204	0.2492	0.1042	0.1457	0.0587	-0.0556	0.2665	-0.0167	0.1278	-4.163	-16.5687	-19.5398
11	20.1702	1.058	9.423	4.8529	1.9643	4.8883	0.3003	-0.7972	-0.2257	0.0118	-0.4263	0.9903	0.0973	-0.598	0.126	0.2075	0.1376	-0.009	0.4258	0.0895	0.5068	-14.8229	-13.8609	-15.3971
12	0.56	-0.2776	0.0542	0.1419	0.0004	0.1945	-0.0538	-0.1101	-0.0244	-0.002	0.0524	0.0115	-0.1829	0.0111	0.0014	0.1944	0.0139	0.0189	0.1301	-0.021	0.0631	21.2546	-29.1081	-28.2028
13	3.5736	-2.1381	-1.5358	2.0492	2.0192	2.5823	-0.1097	0.1448	0.08	0.0067	0.195	0.022	-0.0514	0.2932	-0.0854	0.1351	0.0151	-0.0075	0.1368	0.0418	0.0767	23.2235	-19.632	-22.1536
14	0.8064	1.4158	2.0112	6.733	3.0349	5.0801	-0.0796	0.1084	0.0056	-0.3011	0.0719	-0.0511	-0.197	0.2798	0.0076	0.035	-0.0083	0.0243	0.0514	0.0134	0.0914	30.775	-10.7141	-16.7978
15	3.0944	2.1958	1.1886	3.2426	0.8747	0.8944	0.1491	-0.185	0.0817	0.2524	-0.116	-0.0388	0.0444	-0.0197	-0.0331	0.104	0.0224	0.0302	0.0313	0	0.0296	25.7448	-14.2172	-10.6726
16	2.3897	3.767	2.0965	8.0063	4.0847	3.2718	0.1264	0.233	-0.0984	0.2989	0.0796	-0.5962	0.1234	0.1544	-0.206	0.1619	0.0401	-0.0124	0.1879	0.0221	0.1623	33.1728	-22.2205	-17.8125
17	3.0668	1.36	0.0492	6.4791	0.1514	1.4352	0.0131	0.1027	-0.5948	-0.0047	0.1942	0.1909	0.1773	-0.0727	-0.2072	0.2157	0.0264	0.0286	0.2056	-0.0288	0.2073	19.7111	-24.0806	-17.7129
18	13.4885	8.5724	9.2531	11.6981	8.0615	10.9159	-0.0143	0.1549	-0.0716	-0.0514	0.0874	0.2039	0.0489	0.0521	-0.073	0.1272	0.0906	-0.0025	0.07	-0.0084	0.1618	14.818	-3.0752	-15.4816
19	12.6916	13.0224	-0.132	14.1884	3.2934	14.2626	0.7012	-1.2954	-0.2484	0.7512	-0.9577	-0.2251	0.2582	1.2766	0.2565	0.4608	0.2771	-0.0335	0.978	-0.2573	0.488	25.8884	6.1331	0.2873
20	4.0865	4.2636	3.9368	12.3323	11.1836	15.0263	0.1455	-0.376	0.0158	1.2159	0.2371	0.1364	0.6916	0.3185	-0.3826	0.3862	0.2242	0.0831	0.3549	-0.0979	0.1596	15.1943	7.7443	0.6456
21	15.8901	3.1175	4.4293	2.069	-2.2159	8.4155	-0.2388	-0.5366	0.4331	0.2044	0.0789	0.1068	-0.3226	0.145	0.16	0.3558	0.2983	0.0092	0.6878	0.0075	0.3437	12.4417	9.4698	-8.1721
22	41.1197	7.17	-20.3542	40.0379	-7.6643	10.5132	1.8709	0.5576	2.1569	0.3625	-0.9746	0.0026	-0.8837	-0.1457	-0.8963	0.8695	0.1621	-0.2772	0.6537	-0.2658	0.9763	25.6383	18.1086	-1.8135
23	4.2935	4.5042	5.5854	20.7287	-4.5054	24.0691	-0.1048	-0.054	0.3511	-0.2863	-0.2784	1.1311	-0.1061	-1.0593	0.3831	0.0842	-0.0291	-0.0254	0.2436	0.0031	0.212	-3.672	-32.1054	-7.7562
24	14.8417	3.62	-7.5291	24.7009	-26.396	83.4118	-0.0953	-0.8126	0.1341	1.6592	-0.0337	0.225	-1.2355	-0.4665	0.129	0.1291	0.0046	0.0228	0.0616	-0.0184	0.0134	25.8846	-10.1742	-6.6584

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	389 - 419
2	X-RAY DIFFRACTION	2	A	420 - 430
3	X-RAY DIFFRACTION	3	A	431 - 453
4	X-RAY DIFFRACTION	4	A	454 - 473
5	X-RAY DIFFRACTION	5	A	474 - 495
6	X-RAY DIFFRACTION	6	A	496 - 511
7	X-RAY DIFFRACTION	7	A	512 - 527
8	X-RAY DIFFRACTION	8	A	528 - 547
9	X-RAY DIFFRACTION	9	A	548 - 568
10	X-RAY DIFFRACTION	10	A	569 - 580
11	X-RAY DIFFRACTION	11	A	581 - 598
12	X-RAY DIFFRACTION	12	B	389 - 401
13	X-RAY DIFFRACTION	13	B	402 - 420
14	X-RAY DIFFRACTION	14	B	421 - 431
15	X-RAY DIFFRACTION	15	B	432 - 469
16	X-RAY DIFFRACTION	16	B	470 - 490
17	X-RAY DIFFRACTION	17	B	491 - 524
18	X-RAY DIFFRACTION	18	B	525 - 542
19	X-RAY DIFFRACTION	19	B	543 - 552
20	X-RAY DIFFRACTION	20	B	556 - 580
21	X-RAY DIFFRACTION	21	B	581 - 594
22	X-RAY DIFFRACTION	22	B	595 - 602
23	X-RAY DIFFRACTION	23	C	3 - 10
24	X-RAY DIFFRACTION	24	D	4 - 13

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Yorodumi