PDB-2fsn: Crystal structure of Ta0583, an archaeal actin homolog, complex w...

ID or keywords:

Entry

Database: PDB / ID: 2fsn

Title

Crystal structure of Ta0583, an archaeal actin homolog, complex with ADP

Components

hypothetical protein Ta0583

Hypothesis

Keywords

STRUCTURAL PROTEIN / Actin homolog /

archaea /

ATPase /

MreB / ParM

Function / homology

Function and homology information

Biological species

Thermoplasma acidophilum (acidophilic)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.9 Å

Authors

Roeben, A. / Kofler, C. / Nagy, I. / Nickell, S. / Ulrich Hartl, F. / Bracher, A.

Citation

Journal: J.Mol.Biol. / Year: 2006
Title: Crystal structure of an archaeal actin homolog
Authors: Roeben, A. / Kofler, C. / Nagy, I. / Nickell, S. / Ulrich Hartl, F. / Bracher, A.

History

Deposition	Jan 23, 2006	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Apr 18, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2fsn.cif.gz	125 KB	Display	PDBx/mmCIF format
PDB format	pdb2fsn.ent.gz	101.8 KB	Display	PDB format
PDBx/mmJSON format	2fsn.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/fs/2fsn ftp://data.pdbj.org/pub/pdb/validation_reports/fs/2fsn	HTTPS FTP

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Related structure data

Related structure data	2fsjC 2fskC C: citing same article (ref.)
Similar structure data	4oyd-2 3lfz-d 6iwb-1 5wqg-2 2qgq-4 2qgq-5 2qgq-2 2qgq-7 5wqi-3 2qgq-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

Deposited unit

A: hypothetical protein Ta0583

B: hypothetical protein Ta0583

hetero molecules

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

1

A: hypothetical protein Ta0583

hetero molecules

defined by author
37.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: hypothetical protein Ta0583

hetero molecules

defined by author
37.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	51.703, 92.840, 73.659
Angle α, β, γ (deg.)	90.00, 89.94, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	hypothetical protein Ta0583 / Hypothesis Mass: 37412.434 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Strain: DSM 1728 / Gene: Ta0583 / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Bl21 / References: UniProt: Q9HKL4
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.36 Å³/Da / Density % sol: 47.91 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100mM Bis-Tris pH 6.5, 15-17% PEG-2000MME, 14-16% ethylene glycol, 10mM ADP, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9788 Å
Detector	Type: MARRESEARCH / Detector: CCD / Date: May 6, 2005
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9788 Å / Relative weight: 1
Reflection	Resolution: 2.9→73.659 Å / Num. obs: 15505 / % possible obs: 99.8 % / Redundancy: 3.8 % / R_merge(I) obs: 0.045 / R_sym value: 0.045 / Net I/σ(I): 11
Reflection shell	Resolution: 2.9→3.06 Å / % possible obs: 100 % / Redundancy: 3.8 % / R_merge(I) obs: 0.414 / Mean I/σ(I) obs: 1.4 / Num. measured all: 8454 / Num. unique obs: 2241 / R_sym value: 0.414

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Phasing

Phasing MR

R_factor: 0.521 / Cor.coef. F_o:F_c: 0.468

	Highest resolution	Lowest resolution
Rotation	2.9 Å	57.7 Å
Translation	2.9 Å	57.7 Å

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Processing

Software

Name	Version	Classification
SCALA		data scaling
MOLREP		phasing
REFMAC		refinement
PDB_EXTRACT	1.701	data extraction
MOSFLM		data reduction
CCP4	(SCALA)	data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.9→20 Å / Cor.coef. F_o:F_c: 0.893 / Cor.coef. F_o:F_c free: 0.817 / SU B: 23.419 / SU ML: 0.466 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.575 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.359	771	5 %	RANDOM
R_work	0.283	-	-	-
all	0.287	-	-	-
obs	-	15449	99.84 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 38.473 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.26 Å²	0 Å²	0.3 Å²
2-	-	-0.74 Å²	0 Å²
3-	-	-	5 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4243	0	56	9	4308

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.021	4368
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	3973
X-RAY DIFFRACTION	r_angle_refined_deg	1.869	1.99	5984
X-RAY DIFFRACTION	r_angle_other_deg	0.97	3	9052
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.662	5	616
X-RAY DIFFRACTION	r_chiral_restr	0.088	0.2	717
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	5073
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	820
X-RAY DIFFRACTION	r_nbd_refined	0.262	0.2	1113
X-RAY DIFFRACTION	r_nbd_other	0.239	0.2	4715
X-RAY DIFFRACTION	r_nbtor_other	0.091	0.2	2606
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.191	0.2	124
X-RAY DIFFRACTION	r_metal_ion_refined	0.045	0.2	2
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.273	0.2	11
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.174	0.2	41
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.096	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	0.791	1.5	3061
X-RAY DIFFRACTION	r_mcangle_it	1.453	2	4769
X-RAY DIFFRACTION	r_scbond_it	1.86	3	1307
X-RAY DIFFRACTION	r_scangle_it	3.147	4.5	1214

LS refinement shell

Resolution: 2.9→2.974 Å / Total num. of bins used: 20

	R_factor	Num. reflection
R_free	0.52	56
R_work	0.335	1046
obs	-	1102

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	0.5931	1.3674	0.2728	3.2393	-0.085	2.1823	-0.023	-0.0444	0.1287	-0.0222	-0.1234	-0.0944	-0.1722	0.0729	0.1463	0.2351	-0.0147	-0.0138	0.2649	0.0325	0.2783	4.7187	8.0268	14.0407
2	3.8691	1.9938	0.0303	7.0741	0.2061	-3.4277	1.1743	-0.5608	-0.9496	0.4776	-0.1804	-0.6733	0.0059	-0.1609	-0.9939	0.1769	-0.053	-0.0626	0.4309	0.0856	0.2985	19.231	1.0465	21.0365
3	3.0396	-2.6275	-3.3681	-8.5648	-27.1399	-31.8326	1.2915	0.052	0.1393	-0.2947	0.0533	-0.7642	-1.2082	-0.13	-1.3448	0.2047	-0.1704	-0.0366	0.4098	-0.0351	0.3321	21.4317	10.8158	20.0639
4	3.856	-2.4671	7.0597	1.9858	-1.9876	-0.1761	0.0765	-0.1483	-0.1203	0.0821	0.413	-0.2823	-0.3182	-0.1958	-0.4895	0.1991	-0.1103	-0.0199	0.3615	0.0142	0.3059	21.2595	7.1493	21.6209
5	-7.2102	13.7941	-6.4558	-61.6836	69.9872	-62.2387	0.4382	0.1054	-0.4467	-1.2143	1.5454	1.5308	0.7816	-1.2154	-1.9836	0.239	0.018	0.0333	0.4726	0.2109	0.3494	22.8804	-1.2626	15.6805
6	7.3873	-12.502	6.5764	1.4589	1.8771	0.0951	0.8349	-0.0268	0.305	-0.1919	-0.3179	0.0849	0.2056	0.047	-0.5169	0.173	0.0378	-0.0676	0.3402	0.0854	0.3198	12.3432	-3.861	23.2776
7	10.2609	3.6469	13.6771	5.2609	-16.8132	21.5679	-0.339	-0.6766	0.3646	-0.2432	0.6106	-0.1803	-0.0707	-0.4014	-0.2715	0.1987	0.0538	0.0903	0.311	0.015	0.2228	3.7651	1.2791	27.1221
8	0.4097	0.5375	-1.5708	1.5616	0.1239	5.8141	-0.0467	-0.1965	0.1198	0.0897	-0.0741	-0.4727	-0.5249	0.2074	0.1208	0.2317	-0.0423	-0.0394	0.2979	0.0246	0.316	11.0865	9.9087	20.7101
9	0.0438	-0.2797	-0.2983	-2.4507	-0.9236	1.068	0.0729	-0.412	0.2504	0.3207	-0.095	0.2852	0.0121	0.1472	0.0221	0.2735	0.0164	-0.05	0.2863	0.0139	0.3056	-1.6609	6.9621	22.5821
10	-1.1224	2.5804	-1.7232	6.1789	-3.6802	-1.3665	0.2069	0.0018	0.045	0.5625	-0.3018	0.0645	-0.2028	-0.131	0.0948	0.2829	-0.0164	-0.059	0.3242	-0.0072	0.2715	-1.4512	4.92	30.2638
11	-16.9323	1.4209	7.3475	0.6887	0.4086	-1.9186	-0.3822	0.257	-0.0465	-0.2016	0.1484	-0.2665	-0.3562	-0.1311	0.2338	0.3455	-0.0569	-0.0352	0.2899	-0.0025	0.4029	13.0948	18.1247	23.1943
12	-12.1721	-9.6087	-1.1709	18.8972	7.6926	4.3987	-0.0868	0.0633	-0.1776	0.6246	-0.1988	-0.1013	-0.2087	-0.0157	0.2856	0.2668	0.001	-0.0057	0.2784	0.025	0.2827	-5.5468	9.0248	23.6487
13	0.9642	-1.9796	2.0463	4.2608	-3.1961	0.1947	0.2139	0.0249	0.0974	-0.0138	-0.0921	0.1705	-0.1375	0.075	-0.1218	0.2526	0.0593	-0.0263	0.2871	0.054	0.2856	-10.3712	4.2236	12.1009
14	17.8048	-2.9713	-15.8183	11.9192	-12.4811	6.3379	-0.2962	0.817	-0.2505	-0.2892	0.6567	0.1807	0.5466	-0.8053	-0.3605	0.2416	-0.0703	-0.1418	0.3502	0.0228	0.2168	-19.1003	1.6903	7.9159
15	3.502	-1.233	0.3296	1.8018	0.0556	0.1565	0.0255	-0.2174	0.0566	-0.137	-0.0127	-0.0031	0.0772	-0.0993	-0.0128	0.2861	-0.0112	-0.0029	0.2976	0.0777	0.22	-9.9315	-6.5129	14.8546
16	2.556	-2.2049	-2.0489	3.6024	-1.0168	1.8446	-0.1575	-0.2693	-0.0115	-0.0831	0.248	0.12	0.0686	-0.1378	-0.0905	0.2523	-0.0322	-0.0557	0.2632	0.0086	0.2405	-11.6616	-8.0355	20.1318
17	-2.8967	0.4207	3.3737	5.3657	3.3158	-0.8877	0.2562	-0.1143	-0.1051	-0.3881	0.0436	0.0306	-0.2283	0.3807	-0.2999	0.3945	0.0163	0.0652	0.2946	0.1104	0.2365	12.955	-18.8263	8.4454
18	-32.9468	40.2984	0.8987	-53.7715	-11.1527	-2.9946	2.1889	4.7702	0.7325	1.9186	-4.1222	-1.9954	0.8548	-1.1051	1.9333	0.2737	0.238	0.0459	0.4371	-0.022	0.5422	22.456	-17.242	8.0001
19	-5.5185	-9.6793	-3.3935	2.8607	-1.0811	-7.4568	0.197	0.3284	-0.81	-0.7844	0.0817	-0.6686	-0.0424	1.1095	-0.2787	0.3094	-0.0179	0.1904	0.3069	0.2387	0.3212	13.1917	-10.8044	5.4513
20	-5.8536	-4.0093	-5.3777	-4.1065	5.1829	8.9626	0.1634	0.1806	0.7476	-0.1609	-0.2037	0.2106	-0.6372	0.1077	0.0403	0.3827	0.008	0.1917	0.3068	0.0074	0.2715	19.2151	-13.9301	-0.8132
21	4.8829	2.7293	-2.4186	-0.4233	-2.2211	5.1208	-0.0259	0.3207	-0.3393	-0.1597	-0.0924	-0.1392	0.2645	-0.1493	0.1183	0.3587	0.0049	-0.0159	0.1694	-0.0219	0.3228	-3.7136	-18.9588	9.6813
22	-6.6611	5.4121	4.7223	5.3426	-12.8332	-2.6488	-0.6771	0.478	-0.7171	0.2198	1.0061	1.2043	0.5338	-0.9572	-0.329	0.3518	-0.0253	-0.0813	0.2811	0.0201	0.2997	-21.075	-14.9939	15.0876
23	2.2784	-0.4689	5.4056	-0.1905	0.6403	0.7113	-0.0646	0.2766	-0.2259	-0.4968	-0.0387	-0.0833	0.2382	-0.2636	0.1033	0.3632	-0.0381	-0.0293	0.2314	0.0444	0.2493	-11.8499	-6.7385	8.4007
24	8.2095	2.171	-2.6096	2.3515	0.5239	0.1335	-0.2529	0.671	-0.2374	0.0312	0.287	-0.1226	0.0826	-0.0706	-0.0341	0.3744	-0.037	-0.0367	0.233	0.0272	0.2214	-5.8174	-12.8005	4.7145
25	-7.2693	-3.0403	-1.9119	-8.6724	-0.355	3.4955	-0.0791	0.6118	-0.5258	-0.7347	0.2727	-0.4519	0.217	-0.2581	-0.1936	0.3607	-0.0122	-0.058	0.3006	0.014	0.3713	-10.8926	-5.3948	1.727
26	0.9758	-1.418	0.0533	2.3417	-0.2744	0.1491	-0.0945	-0.0879	0.1287	-0.0809	0.0259	0.0293	-0.0115	0.0874	0.0686	0.2674	-0.0069	-0.0237	0.2513	0.0331	0.298	-3.454	6.6588	11.7238
27	1.0881	1.3393	-1.0251	0.2281	-1.0278	1.3202	0.1123	-0.0765	-0.0628	-0.1293	-0.1437	0.0977	0.2056	-0.1244	0.0314	0.2482	-0.0302	-0.0404	0.2837	-0.0852	0.2808	18.124	2.1899	52.3586
28	1.2241	-0.2001	0.1458	0.6939	-0.2174	0.827	0.0607	-0.1512	-0.0347	0.074	-0.0222	0.0796	0.1875	-0.1572	-0.0385	0.2399	-0.0147	0.0166	0.3181	-0.0362	0.3023	11.0709	3.2346	58.4975
29	0.3138	1.1138	-0.7234	2.0739	-0.6413	0.3263	-0.1652	-0.1396	-0.1833	-0.0719	0.0603	-0.099	0.0597	0.0077	0.1049	0.2884	-0.0081	0.0308	0.2763	-0.0044	0.2914	22.9127	-1.6254	61.9192
30	1.1193	0.4328	0.2589	0.9611	0.4437	0.8689	-0.029	0.0087	0.0018	-0.1832	0.0182	-0.0652	-0.0989	0.1277	0.0107	0.2976	-0.0122	0.0127	0.252	-0.0433	0.2446	36.78	14.9016	48.1399
31	0.9849	-0.7829	0.6915	0.2051	-1.0439	1.1312	0.0895	0.1667	0.2994	-0.1888	-0.0831	0.0058	-0.0647	-0.0988	-0.0064	0.3589	0.0365	-0.0664	0.2271	-0.0633	0.2754	17.2994	25.8374	43.6442
32	1.2813	2.9657	0.4196	-2.1521	-0.0911	3.3991	-0.0689	-0.0746	0.0125	-0.0425	-0.1578	-0.1488	0.1204	-0.0591	0.2266	0.2742	0.0018	0.0119	0.2519	-0.0306	0.2962	30.3651	0.3321	50.944

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 26
2	X-RAY DIFFRACTION	2	A	27 - 32
3	X-RAY DIFFRACTION	3	A	43 - 50
4	X-RAY DIFFRACTION	4	A	51 - 59
5	X-RAY DIFFRACTION	5	A	60 - 64
6	X-RAY DIFFRACTION	6	A	65 - 73
7	X-RAY DIFFRACTION	7	A	74 - 76
8	X-RAY DIFFRACTION	8	A	77 - 94
9	X-RAY DIFFRACTION	9	A	100 - 111
10	X-RAY DIFFRACTION	10	A	112 - 125
11	X-RAY DIFFRACTION	11	A	126 - 144
12	X-RAY DIFFRACTION	12	A	145 - 149
13	X-RAY DIFFRACTION	13	A	150 - 163
14	X-RAY DIFFRACTION	14	A	164 - 169
15	X-RAY DIFFRACTION	15	A	170 - 190
16	X-RAY DIFFRACTION	16	A	191 - 204
17	X-RAY DIFFRACTION	17	A	205 - 221
18	X-RAY DIFFRACTION	18	A	222 - 226
19	X-RAY DIFFRACTION	19	A	227 - 235
20	X-RAY DIFFRACTION	20	A	236 - 248
21	X-RAY DIFFRACTION	21	A	249 - 270
22	X-RAY DIFFRACTION	22	A	271 - 276
23	X-RAY DIFFRACTION	23	A	277 - 285
24	X-RAY DIFFRACTION	24	A	286 - 298
25	X-RAY DIFFRACTION	25	A	299 - 307
26	X-RAY DIFFRACTION	26	A	308 - 325
27	X-RAY DIFFRACTION	27	B	1 - 32
28	X-RAY DIFFRACTION	28	B	43 - 95
29	X-RAY DIFFRACTION	29	B	101 - 150
30	X-RAY DIFFRACTION	30	B	151 - 204
31	X-RAY DIFFRACTION	30	B	270 - 311
32	X-RAY DIFFRACTION	31	B	205 - 269
33	X-RAY DIFFRACTION	32	B	312 - 325

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