PDB-4e81: Crystal structure of the substrate binding domain of E.coli DnaK ...

ID or keywords:

Entry

Database: PDB / ID: 4.0E+81

Title

Crystal structure of the substrate binding domain of E.coli DnaK in complex with a short apidaecin peptide

Components

Chaperone protein DnaK
apidaecin peptide fragment

Keywords

CHAPERONE

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 / inclusion body / heat shock protein binding / protein folding chaperone / ATP-dependent protein folding chaperone / ADP binding ...
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Apis mellifera (honey bee)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Zahn, M. / Straeter, N.

Citation

Journal: Acs Chem.Biol. / Year: 2012
Title: Api88 is a novel antibacterial designer Peptide to treat systemic infections with multidrug-resistant gram-negative pathogens.
Authors: Czihal, P. / Knappe, D. / Fritsche, S. / Zahn, M. / Berthold, N. / Piantavigna, S. / Muller, U. / Van Dorpe, S. / Herth, N. / Binas, A. / Kohler, G. / De Spiegeleer, B. / Martin, L.L. / ...

History

Deposition	Mar 19, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 30, 2012	Provider: repository / Type: Initial release
Revision 1.1	Aug 1, 2012	Group: Database references
Revision 1.2	Nov 15, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Feb 28, 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	4e81.cif.gz	183.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4e81.ent.gz	148.9 KB	Display	PDB format
PDBx/mmJSON format	4e81.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4e81_validation.pdf.gz	456.6 KB	Display	wwPDB validaton report
Full document	4e81_full_validation.pdf.gz	458.6 KB	Display
Data in XML	4e81_validation.xml.gz	20.2 KB	Display
Data in CIF	4e81_validation.cif.gz	28.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/e8/4e81 ftp://data.pdbj.org/pub/pdb/validation_reports/e8/4e81	HTTPS FTP

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Related structure data

Related structure data	1dkx 1dky 1dkz 3dpo 3dpp 3dpq 3qnj
Similar structure data	4ezs-d 4jwc-2 4hyb-2 3dpo-3 4hy9-2 3qnj-1 4jwd-2 3dpq-1 3dpp-1 7jm8-d 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 (11)

Deposited unit

A: Chaperone protein DnaK

B: Chaperone protein DnaK

C: apidaecin peptide fragment

D: apidaecin peptide fragment

hetero molecules

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

1

A: Chaperone protein DnaK

C: apidaecin peptide fragment

hetero molecules

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

2

B: Chaperone protein DnaK

D: apidaecin peptide fragment

hetero molecules

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

Unit cell

Length a, b, c (Å)	144.777, 60.202, 67.453
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: b0014, dnaK, groP, grpF, JW0013, seg / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: P0A6Y8
#2: Protein/peptide	apidaecin peptide fragment Mass: 1210.427 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: The sequence is derived from the antimicrobial peptide apidaecin (honeybee) Source: (synth.) Apis mellifera (honey bee) / References: UniProt: Q06602*PLUS
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.94 Å³/Da / Density % sol: 58.1 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 2.7 M ammonium sulfate, 0.1 M MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 29, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.918 Å / Relative weight: 1
Reflection	Resolution: 1.9→24.34 Å / Num. all: 47233 / Num. obs: 47233 / % possible obs: 99.8 %
Reflection shell	Resolution: 1.9→2 Å / Redundancy: 4.7 % / R_merge(I) obs: 0.53 / Mean I/σ(I) obs: 2.8 / Num. unique all: 6759 / % possible all: 99.1

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Processing

Software

Name	Version	Classification
MAR345		data collection
MOLREP		phasing
REFMAC	5.6.0116	refinement
XDS		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→24.34 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.924 / SU B: 7.005 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25942	2385	5.1 %	RANDOM
R_work	0.20811	-	-	-
obs	0.21072	44719	99.56 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 25.513 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.93 Å²	0 Å²	0 Å²
2-	-	1.47 Å²	0 Å²
3-	-	-	1.46 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→24.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3425	0	15	224	3664

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.019	3498
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.116	1.983	4715
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.587	5	445
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.68	26.329	158
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.48	15	664
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.097	15	18
X-RAY DIFFRACTION	r_chiral_restr	0.144	0.2	557
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.021	2554
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.9→1.949 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.362	156	-
R_work	0.284	2968	-
obs	-	-	97.96 %

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	4.7942	-0.6303	-1.958	0.123	0.51	2.6616	-0.0986	0.2315	-0.2664	0.0257	-0.0062	0.0594	0.1098	-0.0011	0.1048	0.1129	-0.032	0.0759	0.0483	0.0133	0.1518	7.6772	14.7642	13.8551
2	4.4034	-1.9928	0.3772	2.407	1.2276	1.4697	-0.248	-0.0675	0.032	0.1549	0.3249	0.0074	0.1079	0.2982	-0.0769	0.1673	0.0274	-0.001	0.1265	-0.0002	0.1057	20.6038	17.9179	16.7373
3	1.7634	-1.6968	-0.1659	1.7521	0.657	2.3363	-0.0359	0.2039	-0.0802	0.0496	-0.0822	0.1018	0.143	0.2368	0.1181	0.0941	-0.0616	0.0201	0.268	0.0153	0.0191	16.9782	16.091	4.8607
4	4.1743	-1.5038	1.0349	2.7517	-0.3983	1.4531	-0.113	0.0445	0.3425	0.0878	0.1903	0.0704	-0.0665	0.3274	-0.0773	0.0409	-0.023	-0.0015	0.1214	-0.02	0.0665	21.7587	23.4768	14.215
5	4.9023	-0.1716	0.9348	3.0171	1.0147	3.1103	-0.3934	0.0371	0.6745	-0.0541	0.2007	-0.1216	-0.3924	0.0566	0.1927	0.1344	-0.032	-0.0188	0.1534	0.0201	0.1412	18.1555	27.3249	12.2031
6	6.272	-5.1175	-1.9947	15.2058	4.129	1.4848	0.1311	0.6996	-0.5066	-0.107	-0.4406	0.9465	0.1249	-0.4119	0.3095	0.1021	-0.1112	-0.0075	0.2812	-0.0782	0.2055	-0.824	11.316	2.4692
7	21.1729	-0.4089	4.3802	2.0876	-0.28	1.2055	0.0802	-0.2393	-0.4265	0.043	-0.0641	0.2571	0.2521	-0.0077	-0.0161	0.2163	0.0017	0.0883	0.1322	-0.0309	0.0826	20.7068	1.0123	6.1735
8	10.6488	-6.0004	1.3499	6.6984	1.5484	4.0983	-0.0187	0.0744	1.3048	0.0963	-0.0529	-0.5617	-0.1042	0.615	0.0716	0.1928	0.0119	0.0559	0.3362	0.0598	0.2556	48.5697	4.6138	8.7759
9	18.7564	-0.8731	3.0069	1.415	0.466	0.7815	-0.1284	0.6825	0.2348	-0.0316	0.0907	-0.0879	0.0429	0.163	0.0377	0.2186	0.0605	0.0705	0.3253	-0.0193	0.0369	42.2715	-1.91	0.8892
10	5.8486	1.5938	1.3341	1.9249	-0.2298	2.4669	0.1923	-0.0511	-0.5744	0.0965	-0.0186	0.0256	0.0746	0.1796	-0.1737	0.2622	0.0557	0.0318	0.2354	-0.0374	0.101	38.9785	-5.0829	8.505
11	8.9577	7.4079	7.9356	6.6884	6.8461	7.2101	0.0116	0.0882	-0.0632	0.2378	-0.0174	-0.1351	0.0974	-0.0081	0.0058	0.1909	-0.0431	-0.0676	0.1709	-0.0248	0.2594	4.2831	-17.543	14.8449
12	2.107	1.1616	-0.7702	2.2224	0.6336	1.047	-0.0869	0.1762	0.2707	-0.1115	0.0497	0.3669	0.0402	-0.1227	0.0372	0.0944	-0.0116	-0.0802	0.0381	0.0104	0.1354	17.3795	-8.7704	18.597
13	3.7122	1.0377	1.8649	3.3437	0.1484	3.4933	-0.1559	-0.2119	-0.0323	-0.0802	0.0684	0.0527	-0.1641	0.0793	0.0874	0.0605	0.006	0.0042	0.0657	-0.0002	0.0141	33.2123	-5.0777	19.9238
14	3.3714	1.078	-0.5626	1.5018	-0.1821	0.8551	-0.0182	-0.185	0.2955	-0.1175	0.0348	0.2936	0.1136	0.0361	-0.0165	0.0615	0.012	-0.0626	0.029	-0.0245	0.1277	20.5201	-8.307	27.376
15	1.6994	1.3146	-0.7561	2.77	-0.3742	0.6392	-0.1247	0.0856	-0.1695	-0.3227	0.1068	-0.0115	0.093	0.0985	0.0178	0.15	0.0137	-0.0209	0.0685	-0.039	0.0442	29.4036	-12.4876	17.8465
16	7.0536	1.0138	-0.7486	1.7085	0.004	1.0839	-0.1784	-0.0413	0.0522	-0.0943	0.0851	0.2413	0.1998	-0.0307	0.0933	0.1085	0.0037	-0.0521	0.0104	-0.0023	0.0889	18.3005	-14.3088	24.2861
17	11.5932	8.5126	-2.6141	7.07	-1.6338	2.6996	-0.0059	0.3211	0.4812	-0.2118	0.28	0.8368	-0.1655	0.0143	-0.2741	0.0867	-0.0224	-0.0723	0.0798	-0.051	0.4683	16.8245	7.7474	25.1911
18	6.2332	4.0029	2.5469	5.1934	0.7518	3.2071	0.2234	0.2854	-0.6051	0.0577	-0.2393	-0.4941	0.242	0.325	0.0159	0.026	0.0109	0.0112	0.1253	-0.0378	0.1202	44.6006	15.53	23.9275
19	6.0985	0.1046	-0.2249	2.1332	-0.5597	2.3992	0.0833	0.2699	-0.333	-0.0236	-0.1241	0.0882	-0.0587	-0.0443	0.0408	0.0574	-0.0002	-0.0257	0.0441	-0.0373	0.0447	34.4978	18.5275	29.7081
20	14.6645	8.9472	-2.4344	6.019	2.053	23.2773	-0.2435	0.7488	0.2185	-0.2546	0.3011	0.1388	-1.0027	-0.1845	-0.0576	0.1326	-0.059	0.0267	0.5471	0.0237	0.1128	45.4416	22.8024	17.4058

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	389 - 417
2	X-RAY DIFFRACTION	2	A	418 - 431
3	X-RAY DIFFRACTION	3	A	432 - 456
4	X-RAY DIFFRACTION	4	A	457 - 488
5	X-RAY DIFFRACTION	5	A	489 - 507
6	X-RAY DIFFRACTION	6	A	508 - 518
7	X-RAY DIFFRACTION	7	A	519 - 543
8	X-RAY DIFFRACTION	8	A	544 - 558
9	X-RAY DIFFRACTION	9	A	559 - 577
10	X-RAY DIFFRACTION	10	A	578 - 602
11	X-RAY DIFFRACTION	11	B	389 - 397
12	X-RAY DIFFRACTION	12	B	398 - 421
13	X-RAY DIFFRACTION	13	B	422 - 436
14	X-RAY DIFFRACTION	14	B	437 - 459
15	X-RAY DIFFRACTION	15	B	460 - 488
16	X-RAY DIFFRACTION	16	B	489 - 518
17	X-RAY DIFFRACTION	17	B	519 - 538
18	X-RAY DIFFRACTION	18	B	539 - 560
19	X-RAY DIFFRACTION	19	B	561 - 597
20	X-RAY DIFFRACTION	20	B	598 - 603

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