PDB-2y3m: Structure of the extra-membranous domain of the secretin HofQ fro...

ID or keywords:

Entry

Database: PDB / ID: 2y3m

Title

Structure of the extra-membranous domain of the secretin HofQ from Actinobacillus actinomycetemcomitans

Components

PROTEIN TRANSPORT PROTEIN HOFQ

Keywords

TRANSPORT PROTEIN / SECRETIN / DNA UPTAKE / COMPETENCE

Function / homology

Ribosomal Protein S8; Chain: A, domain 1 - #130 / Ribosomal Protein S8; Chain: A, domain 1 - #120 / Ribosomal Protein S8; Chain: A, domain 1 / 2-Layer Sandwich / Alpha Beta / FORMIC ACID / :

Function and homology information

Biological species

AGGREGATIBACTER ACTINOMYCETEMCOMITANS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Tarry, M. / Jaaskelainen, M. / Tuominen, H. / Ihalin, R. / Hogbom, M.

Citation

Journal: J.Mol.Biol. / Year: 2011
Title: The Extra-Membranous Domains of the Competence Protein Hofq Show DNA Binding, Flexibility and a Shared Fold with Type I Kh Domains.
Authors: Tarry, M. / Jaaskelainen, M. / Paino, A. / Tuominen, H. / Ihalin, R. / Hogbom, M.

History

Deposition	Dec 21, 2010	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 27, 2011	Provider: repository / Type: Initial release
Revision 1.1	Aug 31, 2011	Group: Database references / Version format compliance
Revision 1.2	May 8, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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	2y3m.cif.gz	126 KB	Display	PDBx/mmCIF format
PDB format	pdb2y3m.ent.gz	100.7 KB	Display	PDB format
PDBx/mmJSON format	2y3m.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2y3m_validation.pdf.gz	448.9 KB	Display	wwPDB validaton report
Full document	2y3m_full_validation.pdf.gz	449.5 KB	Display
Data in XML	2y3m_validation.xml.gz	12.4 KB	Display
Data in CIF	2y3m_validation.cif.gz	16 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y3/2y3m ftp://data.pdbj.org/pub/pdb/validation_reports/y3/2y3m	HTTPS FTP

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Related structure data

Similar structure data	1mvf-d 3i0n-1 2fbl-d 6lbf-1 3rmr-3 5uwv-3 4y7o-1 5jk9-6 3i0n-2 5sxp-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: PROTEIN TRANSPORT PROTEIN HOFQ

B: PROTEIN TRANSPORT PROTEIN HOFQ

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	119.610, 119.610, 51.280
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	171
Space group name H-M	P6₂

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	5	A	6 - 13
2	1	1	5	B	6 - 13
1	2	1	5	A	37 - 51
2	2	1	5	B	37 - 51
1	3	1	5	A	53 - 62
2	3	1	5	B	53 - 62
1	4	1	5	A	66 - 68
2	4	1	5	B	66 - 68
1	5	1	5	A	107 - 128
2	5	1	5	B	107 - 128
1	6	1	5	A	131 - 142
2	6	1	5	B	131 - 142
1	7	1	5	A	144 - 148
2	7	1	5	B	144 - 148
1	8	1	5	A	70 - 77
2	8	1	5	B	70 - 77
1	9	1	5	A	150 - 161
2	9	1	5	B	150 - 161
1	10	1	5	A	163 - 166
2	10	1	5	B	163 - 166

#1: Protein	PROTEIN TRANSPORT PROTEIN HOFQ / EMHOFQ Mass: 19695.553 Da / Num. of mol.: 2 / Fragment: RESIDUES 27-195 Source method: isolated from a genetically manipulated source Source: (gene. exp.) AGGREGATIBACTER ACTINOMYCETEMCOMITANS (bacteria) Strain: DS7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: C9R226
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH₂O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.61 Å³/Da / Density % sol: 53 % / Description: NONE
Crystal grow	Details: 2 M SODIUM FORMATE, 0.1 M SODIUM ACETATE PH 4.6 .

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
Detector	Type: ADSC QUANTUM 210 / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9334 Å / Relative weight: 1
Reflection	Resolution: 2.3→46 Å / Num. obs: 18861 / % possible obs: 100 % / Redundancy: 7.3 % / R_merge(I) obs: 0.03 / Net I/σ(I): 16.6
Reflection shell	Resolution: 2.3→2.42 Å / Redundancy: 4.9 % / R_merge(I) obs: 0.61 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0102	refinement
MOSFLM		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.3→46 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.928 / SU B: 15.332 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.239 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23669	969	5.1 %	RANDOM
R_work	0.20469	-	-	-
obs	0.2063	17878	99.97 %	-

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: 49.466 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.22 Å²	0.61 Å²	0 Å²
2-	-	1.22 Å²	0 Å²
3-	-	-	-1.83 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→46 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2160	0	15	51	2226

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.022	2200
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.044	1.989	2965
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.103	5	268
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.333	25.833	96
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.577	15	424
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	10.672	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.061	0.2	357
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.021	1572
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	0.218	1.5	1361
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.427	2	2201
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.668	3	839
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.13	4.5	764
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	376	medium positional	0.34	0.5
2	B	376	medium positional	0.34	0.5
1	A	374	loose positional	0.62	5
2	B	374	loose positional	0.62	5
1	A	376	medium thermal	0.27	2
2	B	376	medium thermal	0.27	2
1	A	374	loose thermal	0.3	10
2	B	374	loose thermal	0.3	10

LS refinement shell

Resolution: 2.3→2.36 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.362	73	-
R_work	0.319	1313	-
obs	-	-	99.78 %

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	26.4797	2.8147	-0.2643	38.2754	-8.2632	18.679	0.3874	-0.2241	-1.0097	-0.2618	0.3385	2.8152	1.6367	-1.6905	-0.7259	0.3478	-0.0433	0.0014	0.2312	0.0861	0.3233	-50.1104	-14.481	-8.1813
2	10.0788	-6.7878	1.2269	63.661	-28.6166	20.9663	-0.5579	-0.4294	0.7159	-0.3014	1.3291	1.9753	-0.3721	-0.7442	-0.7712	0.3167	-0.0284	-0.0592	0.0957	-0.0073	0.238	-49.7672	2.4891	-15.2258
3	25.7557	2.9241	-9.2793	2.0136	-2.7141	6.7582	0.3088	-0.7398	0.6765	0.2966	-0.0413	0.4263	-0.4403	0.0848	-0.2676	0.4932	-0.0577	0.0764	0.0887	0.03	0.1825	-44.5876	18.7857	-22.208
4	24.8655	14.2707	7.4763	16.4195	6.7433	9.3969	0.197	-0.4291	0.569	0.1585	-0.3815	1.049	0.3404	-1.3658	0.1845	0.3503	-0.1527	0.0463	0.3683	0.0533	0.1782	-47.0534	21.4843	-31.8831
5	5.5959	-0.2911	-0.2527	9.2185	-6.1168	10.2721	-0.081	-0.0215	0.1304	0.1509	-0.0299	-0.4572	-0.0328	0.6775	0.111	0.255	-0.1087	0.0325	0.158	-0.0247	0.1243	-37.3905	19.4075	-35.7135
6	-1.8413	1.9393	-7.2706	1.258	-10.8001	28.6699	0.181	-0.8106	-0.2638	0.3048	-0.3124	-0.5631	-0.6378	2.1023	0.1314	0.5115	-0.1624	-0.0804	0.2897	0.1834	0.3452	-43.0512	7.8912	-20.5864
7	15.5497	5.7665	-1.9059	7.9303	-3.5939	11.5503	0.6333	-0.0182	1.6507	-0.0355	-0.0389	1.5058	-1.0432	-0.6379	-0.5945	0.3266	0.1829	0.0661	0.1854	0.0712	0.2934	-48.5395	-4.7096	-6.6074
8	13.4971	4.275	1.1874	6.1439	1.8717	10.4748	-0.061	-1.0555	0.3554	0.324	0.2447	0.2987	-0.4851	-0.1142	-0.1837	0.485	0.1111	0.0209	0.068	0.1104	0.2593	-44.5204	-4.251	4.5729
9	4.2353	4.5721	1.7856	17.0373	-0.5415	6.4661	0.1189	0.263	-0.2651	-0.3109	-0.2226	-0.8437	-0.2846	0.3234	0.1037	0.281	0.0966	0.0754	0.1201	0.0327	0.1128	-37.9352	-11.618	-3.8687
10	13.5337	3.2604	-1.5857	12.9981	-5.3026	3.864	-0.015	-0.0558	-0.0599	-0.1866	0.3917	0.6784	-0.1916	-0.3087	-0.3767	0.2652	0.1055	0.0012	0.2261	0.0277	0.0964	-48.1987	-9.3289	-0.6159
11	4.2132	9.0089	-4.671	22.6537	-12.0516	4.621	-0.2002	-0.3431	0.1229	0.183	0.2578	-0.1674	-0.4842	-0.1901	-0.0576	0.6414	0.0609	0.0427	0.1686	0.0221	0.1468	-42.8962	-1.2698	0.2309
12	11.4958	-0.1288	-3.8602	4.0004	-4.6936	9.7881	0.4575	-0.5053	-0.0089	0.2154	-0.2289	-0.1385	-0.7071	0.15	-0.2286	0.4068	0.0404	0.0476	0.1318	0.0094	0.1716	-40.8475	-10.4225	8.8016
13	9.4983	11.6866	-9.1702	34.0911	-25.2405	22.7087	0.4256	0.1279	0.7415	0.7305	0.2197	1.1843	-0.5984	-0.3751	-0.6453	0.3048	-0.0389	0.0436	0.1619	-0.0258	0.0869	-44.4865	21.2895	-40.2707
14	12.1016	3.2785	0.983	57.7655	-24.3901	10.7232	-0.3241	1.2994	-0.7353	-0.1682	1.6413	1.5504	0.2587	1.5714	-1.3172	0.4847	-0.1048	0.0851	0.7857	-0.1635	0.1708	-50.6018	-2.9528	-28.5762
15	21.1765	-16.9668	1.8309	23.2409	-2.735	4.8809	0.3193	0.3584	0.6582	-0.3523	-0.3528	0.0726	-0.2363	0.0055	0.0335	0.2964	0.0116	-0.0164	0.1249	0.0417	0.1965	-54.5026	-0.4449	-19.765
16	1.145	1.098	-2.1458	9.655	-10.5196	16.8161	-0.0208	0.7969	-0.2379	-0.676	-0.1715	-0.4645	0.551	1.104	0.1923	0.2585	0.0713	0.025	0.4485	-0.0292	0.2052	-42.4315	-6.8961	-17.0755
17	1.7803	-8.6298	-4.6386	29.3257	-20.371	20.9352	-0.5398	-0.1478	-0.2232	-0.386	-0.708	-0.8821	1.3407	1.5462	1.2478	0.4903	-0.2186	-0.0738	0.2636	0.1429	0.2723	-44.0831	6.57	-31.8301
18	6.7581	0.2044	-1.5522	38.0421	-11.421	11.1232	0.5424	0.1951	-0.2088	0.3795	0.0181	1.6194	-0.4564	-0.8903	-0.5606	0.2624	-0.0874	0.0637	0.2756	-0.066	0.0613	-44.7364	21.2266	-45.3469
19	5.4158	-3.1214	0.2412	15.7662	-0.8788	5.9012	0.3485	0.1875	-0.0479	-0.2765	-0.3675	1.6153	-0.7697	-2.0017	0.0189	0.2466	0.0451	0.0944	0.5073	0.1073	0.3148	-48.4059	25.6949	-55.8546
20	6.7484	1.8677	1.0138	15.0535	4.4908	10.2163	0.1374	-0.3015	0.0528	0.1523	0.2336	-0.9576	0.3008	0.6635	-0.371	0.2115	-0.0246	0.0355	0.2	0.0426	0.1321	-33.6953	18.6554	-52.2777
21	4.9375	-2.4854	-0.6273	11.3627	-5.176	7.9361	0.1936	-0.1047	0.1001	0.1978	0.068	0.6233	-0.0669	-0.307	-0.2616	0.2354	-0.0945	-0.0003	0.1962	0.0276	0.1474	-42.6182	23.6054	-50.8312
22	4.7364	-7.4219	-0.0138	29.4263	-4.3023	2.3827	0.0323	-0.1558	-0.3153	0.2373	0.1161	0.6887	0.6253	-0.3641	-0.1484	0.3415	-0.1396	-0.0074	0.2891	0.0584	0.0995	-43.0814	16.6521	-53.2557
23	27.0529	-6.1062	-4.8039	23.8021	-10.1086	6.7725	0.4544	0.1781	1.2099	0.217	0.0244	0.0216	-0.7307	-0.0764	-0.4788	0.5162	-0.1462	0.1101	0.1544	0.0263	0.1404	-41.566	29.0246	-62.5752
24	4.3417	-1.0436	-7.0879	17.0533	-11.4735	19.671	-0.2801	0.516	-0.9358	-0.571	0.1738	-0.1683	0.4676	0.3511	0.1063	0.3381	-0.2537	0.0824	0.2615	-0.1673	0.3881	-33.1069	19.4649	-60.4995

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 8
2	X-RAY DIFFRACTION	2	A	9 - 14
3	X-RAY DIFFRACTION	3	A	15 - 26
4	X-RAY DIFFRACTION	4	A	27 - 45
5	X-RAY DIFFRACTION	5	A	46 - 62
6	X-RAY DIFFRACTION	6	A	63 - 69
7	X-RAY DIFFRACTION	7	A	70 - 75
8	X-RAY DIFFRACTION	8	A	76 - 115
9	X-RAY DIFFRACTION	9	A	116 - 129
10	X-RAY DIFFRACTION	10	A	130 - 141
11	X-RAY DIFFRACTION	11	A	142 - 151
12	X-RAY DIFFRACTION	12	A	152 - 168
13	X-RAY DIFFRACTION	13	B	28 - 36
14	X-RAY DIFFRACTION	14	B	37 - 49
15	X-RAY DIFFRACTION	15	B	50 - 68
16	X-RAY DIFFRACTION	16	B	69 - 85
17	X-RAY DIFFRACTION	17	B	86 - 92
18	X-RAY DIFFRACTION	18	B	93 - 98
19	X-RAY DIFFRACTION	19	B	99 - 132
20	X-RAY DIFFRACTION	20	B	133 - 153
21	X-RAY DIFFRACTION	21	B	154 - 165
22	X-RAY DIFFRACTION	22	B	166 - 174
23	X-RAY DIFFRACTION	23	B	175 - 181
24	X-RAY DIFFRACTION	24	B	182 - 191

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-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

-
Basic information

-
Structure visualization

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Downloads & links

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Download

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Validation report

-
Related structure data

-
Links

-
Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi