PDB-3dqg: Peptide-binding domain of heat shock 70 kDa protein F, mitochondr...

ID or keywords:

Entry

Database: PDB / ID: 3dqg

Title

Peptide-binding domain of heat shock 70 kDa protein F, mitochondrial precursor, from Caenorhabditis elegans.

Components

Heat shock 70 kDa protein F

Keywords

CHAPERONE /

structural genomics / APC90008.12 /

Hsp70 protein / peptide-binding domain / PSI-2 /

Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / ATP-binding /

Mitochondrion / Nucleotide-binding /

Stress response / Transit peptide

Function / homology

Function and homology information

mitochondrial unfolded protein response /

misfolded protein binding / chaperone cofactor-dependent protein refolding / response to unfolded protein / cellular response to unfolded protein / protein folding chaperone /

heat shock protein binding / unfolded protein binding / protein refolding /

ATP hydrolysis activity ...
Similarity search - Function

Biological species

Caenorhabditis elegans (invertebrata)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.72 Å

Authors

Osipiuk, J. / Mulligan, R. / Gu, M. / Voisine, C. / Morimoto, R.I. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: X-ray crystal structure of peptide-binding domain of heat shock 70 kDa protein F, mitochondrial precursor, from Caenorhabditis elegans.
Authors: OSIPIUK, J. / MULLIGAN, R. / GU, M. / VOISINE, C. / MORIMOTO, R.I. / JOACHIMIAK, A.

History

Deposition	Jul 9, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 22, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software
Revision 1.3	Aug 30, 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	3dqg.cif.gz	139.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3dqg.ent.gz	112.8 KB	Display	PDB format
PDBx/mmJSON format	3dqg.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/dq/3dqg ftp://data.pdbj.org/pub/pdb/validation_reports/dq/3dqg	HTTPS FTP

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Related structure data

Related structure data	2op6S 3dob S: Starting model for refinement
Similar structure data	2vza-1 4nct-4 2cz5-d 4uiq-d 4hn2-d 2vza-6 1h7s-1 5r90-d 5ra0-d 2vza-8 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
Other databases	TargetDB: APC90008.12

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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: Heat shock 70 kDa protein F

B: Heat shock 70 kDa protein F

C: Heat shock 70 kDa protein F

D: Heat shock 70 kDa protein F

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

1

A: Heat shock 70 kDa protein F

B: Heat shock 70 kDa protein F

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

2

C: Heat shock 70 kDa protein F

D: Heat shock 70 kDa protein F

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

Unit cell

Length a, b, c (Å)	90.418, 120.159, 56.770
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-665- HOH

Details

authors state that the biological unit is experimentally unknown.

#1: Protein	Heat shock 70 kDa protein F Mass: 16209.280 Da / Num. of mol.: 4 / Fragment: peptide-binding domain, residues 418-565 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Strain: Bristol N2 / Gene: hsp-6, hsp70f, C37H5.8 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11141
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 522 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Heat shock 70 kDa protein F

Mass: 16209.280 Da / Num. of mol.: 4 / Fragment: peptide-binding domain, residues 418-565
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Caenorhabditis elegans (invertebrata) / Strain: Bristol N2 / Gene: hsp-6, hsp70f, C37H5.8 / Plasmid: pMCSG7 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11141

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 522 / 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: 2.38 Å³/Da / Density % sol: 48.28 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2 M ammonium sulfate, 20% PEG-4000, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 2, 2007
Radiation	Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 1.72→37.6 Å / Num. all: 63652 / Num. obs: 63652 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / B_iso Wilson estimate: 29.6 Å² / R_merge(I) obs: 0.061 / Χ²: 1.073 / Net I/σ(I): 11.4
Reflection shell	Resolution: 1.72→1.76 Å / Redundancy: 3.9 % / R_merge(I) obs: 0.551 / Mean I/σ(I) obs: 1.92 / Num. unique all: 2798 / Χ²: 0.932 / % possible all: 64.3

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	1.93 Å	37.54 Å
Translation	1.93 Å	37.54 Å

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MOLREP		phasing
REFMAC		refinement
PDB_EXTRACT	3.006	data extraction
SBC-Collect		data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2OP6.pdb

2op6

Resolution: 1.72→37.5 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.948 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.852 / SU B: 4.604 / SU ML: 0.078 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.119 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.216	3230	5.1 %	RANDOM
R_work	0.183	-	-	-
all	0.184	63579	-	-
obs	0.184	63579	95.5 %	-

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 max: 116.19 Å² / B_iso mean: 17.35 Å² / B_iso min: 6.06 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.26 Å²	0 Å²	0 Å²
2-	-	-1.13 Å²	0 Å²
3-	-	-	2.39 Å²

Refinement step

Cycle: LAST / Resolution: 1.72→37.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4387	0	0	522	4909

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	4843
X-RAY DIFFRACTION	r_angle_refined_deg	1.575	1.98	6623
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.8	5	689
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	42.903	26.842	228
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.81	15	968
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.226	15	28
X-RAY DIFFRACTION	r_chiral_restr	0.116	0.2	793
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	3656
X-RAY DIFFRACTION	r_nbd_refined	0.213	0.2	2278
X-RAY DIFFRACTION	r_nbtor_refined	0.303	0.2	3284
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.146	0.2	479
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.203	0.2	88
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.187	0.2	31
X-RAY DIFFRACTION	r_mcbond_it	0.965	1.5	3174
X-RAY DIFFRACTION	r_mcangle_it	1.373	2	5075
X-RAY DIFFRACTION	r_scbond_it	2.474	3	1798
X-RAY DIFFRACTION	r_scangle_it	4.034	4.5	1490

LS refinement shell

Resolution: 1.719→1.764 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.314	150	-
R_work	0.3	2982	-
all	-	3132	-
obs	-	3132	64.68 %

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	0.981	0.5294	0.7006	0.7769	0.5621	3.4608	-0.0647	-0.0101	-0.1065	0.0614	0.0173	-0.086	0.0102	0.1481	0.0474	0.0433	0.0043	-0.0108	0.0441	0.0183	0.0712	32.582	45.7778	82.0008
2	0.4929	0.1759	-0.6765	0.8239	0.4053	1.478	-0.1015	-0.1587	-0.3583	-0.0982	-0.092	-0.0679	-0.0388	0.1	0.1935	0.0388	0.0088	-0.0168	0.0588	0.0646	0.0885	40.729	43.0785	81.9239
3	0.4757	0.29	0.1898	0.255	-0.067	0.5027	-0.0195	0.0034	-0.069	0.0121	0.0409	-0.0061	-0.0184	0.0306	-0.0213	0.0463	0.0008	-0.0052	0.0375	0.0012	0.0755	32.4277	49.0354	71.7674
4	1.2619	0.1574	-0.8811	1.2419	0.5814	1.0062	-0.0524	-0.001	-0.0628	-0.0226	0.164	-0.0669	-0.112	0.179	-0.1116	0.0438	0.0121	-0.0129	0.0474	-0.0039	0.0515	39.6771	53.0024	68.5396
5	7.6141	2.1415	-0.5604	1.0992	-0.4869	4.3184	0.4211	-0.7085	0.6618	0.438	-0.3304	0.2983	-0.3685	-0.0121	-0.0908	0.0814	0.0308	0.0416	0.0975	-0.0108	0.0237	27.0467	47.7321	93.5967
6	2.7989	-0.1304	-1.7831	1.9625	2.4031	4.0951	0.0115	-0.2044	0.1065	-0.0289	0.1877	-0.304	0.0958	0.2492	-0.1993	0.0306	0.0076	0.0003	0.0732	0.0106	0.0919	22.5638	32.7431	70.9624
7	3.8745	1.5886	2.5121	2.8611	1.9269	3.6828	-0.0131	0.2758	-0.0258	-0.3279	0.0792	-0.1129	-0.058	0.0589	-0.066	0.0842	-0.0145	-0.0029	0.0474	0.0246	0.0558	10.2318	35.0541	57.7964
8	6.8185	4.0022	5.1645	3.0807	2.8459	6.0479	-0.3548	0.4031	-0.0145	-0.2972	0.1655	-0.009	-0.4865	0.1786	0.1893	0.069	-0.0225	0.0043	0.0787	-0.0247	0.0372	10.1228	24.5961	57.3045
9	0.9459	0.2215	0.0834	0.0626	-0.0114	0.0966	0.0065	-0.0301	-0.0563	0.0001	0.0054	0.0203	-0.0239	0.0348	-0.0119	0.0465	-0.0026	-0.0161	0.0439	0.007	0.0652	10.6837	31.6235	69.7088
10	1.4239	0.2794	0.4544	0.5855	-0.4453	0.6834	-0.1074	0.0338	0.0526	-0.0868	0.0702	0.1025	0.0253	0.0025	0.0372	0.0537	0.0084	-0.0292	0.0292	0.0107	0.0545	1.7941	36.139	59.021
11	3.1982	-1.0025	5.3593	0.8695	-1.1359	10.3646	-0.2374	-0.1278	0.3658	-0.0753	-0.0338	0.0069	-0.1344	-0.2054	0.2711	0.0665	-0.0314	-0.0197	-0.0045	0.0375	0.1141	16.1493	51.3672	58.1979
12	3.5602	1.3402	0.0258	0.5492	0.3285	2.2757	-0.1405	-0.033	-0.4186	0.3675	0.0838	-0.7163	0.183	0.1351	0.0567	0.0468	0.0074	0.0337	0.041	-0.0117	0.1123	28.3844	33.2943	69.9089
13	3.7741	0.4872	-1.234	4.6853	-2.5506	4.7358	-0.1795	0.6871	-0.0628	-0.6487	0.2406	-0.1461	0.2654	0.1975	-0.0611	0.1813	-0.1122	0.0323	0.2774	-0.0394	0.1169	36.3865	20.2058	29.7809
14	9.727	1.8119	-7.5837	9.8916	1.7792	12.5105	0.0086	0.6919	-0.4207	-1.3439	-0.0016	-0.3551	-0.2761	0.6452	-0.007	0.2631	-0.121	-0.0553	0.3081	0.0834	0.0356	35.1776	29.2765	25.1157
15	1.2708	0.8908	0.0849	0.7946	0.3008	0.3476	-0.1402	0.1178	0.0342	-0.0164	0.1602	-0.0113	0.0169	0.0186	-0.02	0.0478	-0.0202	0.0148	0.0448	0.0075	0.0557	34.1034	24.6007	41.9463
16	6.6356	-0.8818	0.1351	6.9906	1.7896	0.4781	-0.1305	0.8209	0.0643	-0.8566	0.2393	-0.2851	-0.3666	0.1237	-0.1088	0.1643	-0.0886	0.0147	0.1521	0.0456	0.0286	39.0451	34.3747	35.8649
17	4.0225	3.3514	-1.1654	6.0734	0.5748	3.6788	-0.4187	0.2104	-0.6199	-0.7106	0.157	-1.1796	-0.1255	0.9127	0.2617	0.1953	-0.0045	0.0432	0.3989	-0.0102	0.4219	35.1416	8.1028	30.1222
18	4.9331	4.9731	-0.0333	18.5571	-0.7549	7.0055	0.1038	0.2199	0.7473	0.1616	-0.34	1.3291	-0.3521	-0.4452	0.2361	-0.0033	-0.0133	-0.0203	0.0896	-0.0094	0.1647	17.3725	24.0619	42.2427
19	3.0126	0.5042	-1.4018	0.868	0.1087	3.0852	-0.0045	-0.0641	-0.0846	0.1042	-0.0426	0.0127	-0.092	-0.0535	0.0471	0.0502	0.0029	0.0001	0.0083	0.0025	0.0633	13.3343	12.3631	57.0687
20	0.8448	-0.2545	0.641	0.238	0.1051	1.0375	-0.0348	-0.0592	0.0511	-0.0083	-0.0288	-0.0192	-0.1132	-0.0506	0.0635	0.0612	-0.0069	0.0064	0.0231	-0.029	0.0858	9.6579	15.7306	54.6207
21	0.4367	0.2415	-0.1709	0.147	0.004	0.787	-0.0016	0.0248	-0.0027	0	0.0498	-0.0079	-0.0464	0.0159	-0.0482	0.0622	0.0005	0.0083	0.0244	-0.0046	0.0737	15.8631	8.1914	45.0903
22	0.5854	-0.1944	0.9906	0.5816	-0.5943	1.8125	0.0169	0.1382	0.0428	0.1304	0.0364	0.1586	-0.0082	-0.0329	-0.0533	0.065	0.0124	0.0165	0.0636	0.0078	0.0611	7.2051	8.2083	38.4547
23	3.5842	5.0459	6.8541	7.1038	9.6495	13.1073	0.3514	-0.8606	-0.396	1.4284	-0.4066	-0.9201	1.6137	-0.9424	0.0552	0.4425	0.0164	-0.0948	0.4364	-0.0526	0.3632	10.4331	4.6705	62.7211
24	2.4685	0.8474	-0.8579	1.4838	0.3702	2.3404	0.0178	-0.2268	-0.135	0.1526	-0.0379	-0.0471	0.2439	0.1846	0.0201	0.1032	0.0049	-0.0111	0.0529	-0.021	0.1664	26.0193	19.094	56.6485

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	418 - 434	4 - 20
2	X-RAY DIFFRACTION	2	A	A	435 - 449	21 - 35
3	X-RAY DIFFRACTION	3	A	A	450 - 514	36 - 100
4	X-RAY DIFFRACTION	4	A	A	515 - 527	101 - 113
5	X-RAY DIFFRACTION	5	A	A	528 - 552	114 - 138
6	X-RAY DIFFRACTION	6	A	A	553 - 565	139 - 151
7	X-RAY DIFFRACTION	7	B	B	418 - 442	4 - 28
8	X-RAY DIFFRACTION	8	B	B	443 - 449	29 - 35
9	X-RAY DIFFRACTION	9	B	B	450 - 516	36 - 102
10	X-RAY DIFFRACTION	10	B	B	517 - 544	103 - 130
11	X-RAY DIFFRACTION	11	B	B	545 - 555	131 - 141
12	X-RAY DIFFRACTION	12	B	B	556 - 565	142 - 151
13	X-RAY DIFFRACTION	13	C	C	418 - 440	4 - 26
14	X-RAY DIFFRACTION	14	C	C	441 - 449	27 - 35
15	X-RAY DIFFRACTION	15	C	C	450 - 502	36 - 88
16	X-RAY DIFFRACTION	16	C	C	503 - 525	89 - 111
17	X-RAY DIFFRACTION	17	C	C	526 - 556	112 - 142
18	X-RAY DIFFRACTION	18	C	C	557 - 565	143 - 151
19	X-RAY DIFFRACTION	19	D	D	415 - 432	1 - 18
20	X-RAY DIFFRACTION	20	D	D	433 - 449	19 - 35
21	X-RAY DIFFRACTION	21	D	D	450 - 509	36 - 95
22	X-RAY DIFFRACTION	22	D	D	510 - 523	96 - 109
23	X-RAY DIFFRACTION	23	D	D	524 - 535	110 - 121
24	X-RAY DIFFRACTION	24	D	D	536 - 563	122 - 149

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