PDB-3res: Crystal structure of E coli Hfq in complex with ADP

ID or keywords:

Entry

Database: PDB / ID: 3res

Title

Crystal structure of E coli Hfq in complex with ADP

Components

Protein hfq

Keywords

CHAPERONE / ADP / Hfq / Sm fold / RNA Chaperone / RNA binding

Function / homology

Function and homology information

sRNA-mediated post-transcriptional gene silencing / positive regulation of translation, ncRNA-mediated / RNA folding chaperone / regulation of translation, ncRNA-mediated / bent DNA binding / regulation of RNA stability / regulation of DNA-templated transcription / DNA binding / RNA binding / cytosol
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2 Å

Authors

Wang, W.W. / Wu, J.H. / Shi, Y.Y.

Citation

Journal: Genes Dev. / Year: 2011
Title: Cooperation of Escherichia coli Hfq hexamers in DsrA binding.
Authors: Wang, W. / Wang, L. / Zou, Y. / Zhang, J. / Gong, Q. / Wu, J. / Shi, Y.

History

Deposition	Apr 5, 2011	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Oct 19, 2011	Provider: repository / Type: Initial release
Revision 1.1	Mar 20, 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	3res.cif.gz	303.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3res.ent.gz	249.6 KB	Display	PDB format
PDBx/mmJSON format	3res.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3res_validation.pdf.gz	2.9 MB	Display	wwPDB validaton report
Full document	3res_full_validation.pdf.gz	2.9 MB	Display
Data in XML	3res_validation.xml.gz	32.4 KB	Display
Data in CIF	3res_validation.cif.gz	45.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/re/3res ftp://data.pdbj.org/pub/pdb/validation_reports/re/3res	HTTPS FTP

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Related structure data

Related structure data	3rerC C: citing same article (ref.)
Similar structure data	4qvc-d 4qvd-d 3qsu-1 1kq2-d 4ht8-d 3qo3-d 3qsu-3 3qsu-2 1kq1-2 4ht9-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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) #107 - Nov 2008 Mechanosensitive Channels similarity (1) #245 - May 2020 Spliceosomes similarity (1)

Deposited unit

A: Protein hfq

B: Protein hfq

C: Protein hfq

D: Protein hfq

E: Protein hfq

F: Protein hfq

G: Protein hfq

H: Protein hfq

I: Protein hfq

J: Protein hfq

K: Protein hfq

L: Protein hfq

hetero molecules

91.3 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Protein hfq

B: Protein hfq

C: Protein hfq

D: Protein hfq

E: Protein hfq

F: Protein hfq

hetero molecules

defined by author&software
45.7 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

G: Protein hfq

H: Protein hfq

I: Protein hfq

J: Protein hfq

K: Protein hfq

L: Protein hfq

hetero molecules

defined by author&software
45.7 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	111.260, 34.120, 200.743
Angle α, β, γ (deg.)	90.00, 98.39, 90.00
Int Tables number	5
Space group name H-M	I121

#1: Protein	Protein hfq / HF-1 / Host factor-I protein Mass: 7325.554 Da / Num. of mol.: 12 / Fragment: UNP residues 1-65 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: BL21 / Gene: B21_04001, hfq / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C5W5L7, UniProt: P0A6X3*PLUS
#2: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / DsrA sRNA Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.14 Å³/Da / Density % sol: 42.63 % / Mosaicity: 0.78 °
Crystal grow	Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 200mM NH4Ac, 100mM NaAc, 22% PEG 4000, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL17U / Wavelength: 0.9793 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 2, 2010

Radiation

Monochromator: plane grating / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9793 Å / Relative weight: 1

Reflection

Resolution: 1.9→102.843 Å / Num. all: 58163 / Num. obs: 58163 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.4 % / B_iso Wilson estimate: 36 Å² / R_merge(I) obs: 0.074 / R_sym value: 0.074 / Net I/σ(I): 12

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) all	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_pim(I) all	R_rim(I) all	R_sym value	Net I/σ(I) obs	% possible all
1.9-2	5.3	0.227	0.205	3.1	43499	8256	0.095	0.227	0.205	5.3	95.6
2-2.12	5.3	0.178	0.161	3.1	41868	7896	0.075	0.178	0.161	6.6	96.6
2.12-2.27	5.3	0.128	0.116	3	39974	7476	0.054	0.128	0.116	8.8	97.4
2.27-2.45	5.5	0.104	0.094	6.6	38340	7015	0.044	0.104	0.094	10.1	98
2.45-2.69	5.6	0.097	0.088	6.3	36195	6498	0.041	0.097	0.088	11.7	98.6
2.69-3	5.6	0.085	0.077	6.9	33247	5906	0.035	0.085	0.077	14.3	98.6
3-3.47	5.6	0.079	0.072	7.1	29569	5266	0.033	0.079	0.072	18	98.9
3.47-4.25	5.6	0.074	0.067	7.4	25102	4504	0.031	0.074	0.067	21	99.1
4.25-6.01	5.5	0.064	0.057	8	19011	3460	0.027	0.064	0.057	22.4	98.6
6.01-30.576	5.2	0.061	0.054	8.6	9730	1886	0.027	0.061	0.054	20	93.2

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

R_factor: 63.88 / Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.5 Å	30.58 Å
Translation	2.5 Å	30.58 Å

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA	3.3.16	data scaling
PHASER	2.1.4	phasing
REFMAC		refinement
PDB_EXTRACT	3.1	data extraction
HKL-2000		data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→102.84 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.939 / WR_factor R_free: 0.2753 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.791 / SU B: 10.099 / SU ML: 0.127 / SU R_free: 0.1625 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.211 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23864	2543	5.1 %	RANDOM
R_work	0.19861	-	-	-
obs	0.20072	47552	97.26 %	-

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 max: 117.16 Å² / B_iso mean: 34.662 Å² / B_iso min: 4.3 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.45 Å²	0 Å²	-0.7 Å²
2-	-	4.37 Å²	0 Å²
3-	-	-	-3.13 Å²

Refinement step

Cycle: LAST / Resolution: 2→102.84 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5579	0	216	283	6078

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	5985
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.483	2.009	8182
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.959	5	736
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.952	24.703	219
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.375	15	984
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.861	15	23
X-RAY DIFFRACTION	r_chiral_restr	0.095	0.2	1000
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	4294
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	0.599	1.5	3689
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.065	2	6045
X-RAY DIFFRACTION	r_scbond_it	1.831	3	2296
X-RAY DIFFRACTION	r_scangle_it	2.989	4.5	2134
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2→2.052 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.282	162	-
R_work	0.219	3435	-
obs	-	-	95.97 %

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	5.1083	-2.7504	1.7624	4.0878	-1.7026	5.3842	-0.5038	-0.9999	-0.0886	0.5878	0.5805	0.1279	-0.3255	-0.732	-0.0767	0.17	0.0807	0.0425	0.2372	0.0148	0.0325	35.35	-2.4282	44.103
2	5.7219	-1.4284	0.1742	2.4349	-0.4855	5.5582	-0.0898	-0.2869	-0.1057	0.2846	-0.0838	-0.0533	0.3085	0.3694	0.1736	0.1351	-0.0137	-0.0144	0.0545	0.0318	0.0815	51.0003	-6.1379	35.9257
3	3.8524	-0.4816	1.0784	1.1786	-0.5399	7.8015	0.0675	0.3085	-0.0792	0.0056	-0.0743	-0.1825	0.3092	0.8915	0.0068	0.0495	0.028	0.0172	0.1287	0.0235	0.1222	52.0171	-4.3415	17.6449
4	3.7107	-0.028	1.9635	1.2668	-0.3013	5.0814	-0.0651	0.2265	0.1176	-0.0257	-0.0715	-0.031	-0.1323	0.373	0.1366	0.0551	-0.0051	0.0121	0.0333	0.0233	0.0836	37.4921	1.6475	7.3511
5	3.2937	0.1929	-0.278	1.4597	0.1451	5.552	-0.0952	-0.1923	0.1934	-0.0426	-0.0259	0.0857	-0.3251	-0.6989	0.1212	0.0715	0.0589	-0.0134	0.1087	-0.0438	0.1039	21.8342	5.9146	16.1566
6	5.2183	0.4747	-2.506	1.7553	0.6818	5.1686	-0.1474	-0.3985	0.0344	0.1061	-0.1627	0.2589	0.0808	-0.3601	0.3101	0.0486	0.0365	0.0319	0.1501	-0.0548	0.0762	20.3013	3.7664	34.9429
7	4.2646	0.9882	0.7816	1.4445	1.1808	4.0707	-0.0723	0.4529	-0.1175	-0.4588	-0.0336	-0.0821	-0.07	0.4052	0.1058	0.2056	0.0985	0.0383	0.1599	0.0397	0.0374	20.5587	-0.4705	-44.4144
8	5.8986	2.5372	0.0543	3.1381	0.1574	5.7691	0.0517	0.2064	-0.1664	-0.42	-0.218	0.0279	0.3351	-0.5975	0.1662	0.1692	0.0961	-0.043	0.2114	-0.0501	0.0708	5.308	-6.0058	-36.0865
9	2.7569	0.0722	1.9759	1.0404	0.1249	12.3381	0.1809	-0.3375	-0.1714	-0.097	-0.126	0.1837	0.7728	-1.5838	-0.055	0.0689	-0.1023	-0.0058	0.3427	-0.0105	0.1032	4.0037	-5.3345	-17.7468
10	3.4314	0.1711	1.788	0.767	0.2184	5.0558	-0.0181	-0.1301	0.0259	-0.0047	-0.0738	0.0516	-0.0587	-0.4391	0.0919	0.0072	0.0097	0.0099	0.0455	-0.004	0.0238	17.8958	1.1843	-7.3017
11	4.3487	-0.155	0.5798	1.6155	-0.4269	6.6946	-0.1528	0.3432	0.2402	0.06	-0.0953	-0.1396	-0.4535	0.6896	0.2481	0.0601	-0.0463	-0.0143	0.1108	0.0726	0.0728	33.1285	7.171	-15.9237
12	3.633	-0.1674	-1.7131	1.8658	-0.4431	6.6088	-0.0431	0.0934	0.0325	-0.122	-0.2238	-0.2337	-0.1425	0.7475	0.2669	0.0444	-0.0125	0.0205	0.3146	0.1262	0.0691	34.9339	5.7209	-34.5588

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 65
2	X-RAY DIFFRACTION	2	B	6 - 65
3	X-RAY DIFFRACTION	3	C	5 - 65
4	X-RAY DIFFRACTION	4	D	5 - 65
5	X-RAY DIFFRACTION	5	E	6 - 65
6	X-RAY DIFFRACTION	6	F	6 - 65
7	X-RAY DIFFRACTION	7	G	6 - 65
8	X-RAY DIFFRACTION	8	H	6 - 65
9	X-RAY DIFFRACTION	9	I	6 - 65
10	X-RAY DIFFRACTION	10	J	5 - 65
11	X-RAY DIFFRACTION	11	K	6 - 65
12	X-RAY DIFFRACTION	12	L	6 - 65

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