PDB-2gwk: SpvB ADP-ribosylated actin: orthorhombic crystal form

ID or keywords:

Entry

Database: PDB / ID: 2gwk

Title

SpvB ADP-ribosylated actin: orthorhombic crystal form

Components

Actin, alpha skeletal muscle

Keywords

CONTRACTILE PROTEIN /

actin /

ADP-ribosylation

Function / homology

Function and homology information

cytoskeletal motor activator activity /

tropomyosin binding /

myosin heavy chain binding / mesenchyme migration /

troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament ...
Similarity search - Function

Biological species

Oryctolagus cuniculus (rabbit)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Stebbins, C.E. / Margarit, S.M.

Citation

Journal: Structure / Year: 2006
Title: A steric antagonism of actin polymerization by a salmonella virulence protein.
Authors: Margarit, S.M. / Davidson, W. / Frego, L. / Stebbins, C.E.

History

Deposition	May 4, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 29, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2gwk.cif.gz	166.3 KB	Display	PDBx/mmCIF format
PDB format	pdb2gwk.ent.gz	138.1 KB	Display	PDB format
PDBx/mmJSON format	2gwk.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/gw/2gwk ftp://data.pdbj.org/pub/pdb/validation_reports/gw/2gwk	HTTPS FTP

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Related structure data

Related structure data	2gwjC 2gwlC 2gwmC C: citing same article (ref.)
Similar structure data	1lcu-d 1rfq-d 4yvi-d 6izv-d 4gdk-d 6jxn-d 4g0b-3 4yvk-d 5nmw-1 4ade-d 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	#19 - Jul 2001 Actin similarity (10) #18 - Jun 2001 Myosin similarity (9) #241 - Jan 2020 Twenty Years of Molecules similarity (3)

Deposited unit

A: Actin, alpha skeletal muscle

B: Actin, alpha skeletal muscle

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	100.385, 102.348, 123.803
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Actin, alpha skeletal muscle / / Alpha-actin-1 Mass: 41387.227 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃ / Comment: ATP, energy-carrying molecule*YM
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 618 / 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: 3.84 Å³/Da / Density % sol: 67.97 %

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Data collection

Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.979 Å
Detector	Date: Oct 29, 2004
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2→99 Å / Num. obs: 85152

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Processing

Software

Name	Version	Classification	NB
REFMAC	5.2.0005	refinement
PDB_EXTRACT	2	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→32 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.942 / SU B: 6.683 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.211	4084	5.1 %	RANDOM
R_work	0.171	-	-	-
all	0.173	-	-	-
obs	0.172	80138	92.47 %	-

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: 33.432 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.37 Å²	0 Å²	0 Å²
2-	-	0.13 Å²	0 Å²
3-	-	-	0.23 Å²

Refinement step

Cycle: LAST / Resolution: 2→32 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5708	0	64	618	6390

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.022	5897
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	5329
X-RAY DIFFRACTION	r_angle_refined_deg	1.835	1.983	8001
X-RAY DIFFRACTION	r_angle_other_deg	1.217	3	12417
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.297	5	720
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.824	23.944	251
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.685	15	1008
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.152	15	36
X-RAY DIFFRACTION	r_chiral_restr	0.11	0.2	890
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	6446
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1162
X-RAY DIFFRACTION	r_nbd_refined	0.246	0.2	1273
X-RAY DIFFRACTION	r_nbd_other	0.212	0.2	5519
X-RAY DIFFRACTION	r_nbtor_refined	0.181	0.2	2862
X-RAY DIFFRACTION	r_nbtor_other	0.093	0.2	3262
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.218	0.2	487
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.29	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.049	0.2	7
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.209	0.2	22
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.28	0.2	57
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.199	0.2	20
X-RAY DIFFRACTION	r_mcbond_it	1.004	1.5	3757
X-RAY DIFFRACTION	r_mcbond_other	0.273	1.5	1481
X-RAY DIFFRACTION	r_mcangle_it	1.343	2	5862
X-RAY DIFFRACTION	r_scbond_it	2.593	3	2511
X-RAY DIFFRACTION	r_scangle_it	3.642	4.5	2139

LS refinement shell

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

	R_factor	Num. reflection	% reflection
R_free	0.273	309	-
R_work	0.208	5324	-
obs	-	5633	89.26 %

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	2.5662	-0.8479	0.9242	2.0736	-0.3611	2.8305	-0.0104	0.1118	-0.1763	-0.1661	-0.0332	0.2388	0.0723	-0.1991	0.0436	-0.2185	-0.0314	-0.0232	-0.1344	-0.0105	-0.1142	30.907	20.177	55.422
2	3.2487	-1.155	-1.1261	1.2067	0.9099	0.8719	-0.1038	-0.138	0.1176	0.0559	0.0556	-0.0276	-0.1399	0.0074	0.0483	-0.1956	-0.0218	-0.027	-0.1364	0.0175	-0.1478	40.624	25.289	66.56
3	5.7178	0.6833	1.6514	3.1379	0.455	4.1317	-0.1722	0.0831	0.0659	-0.0091	0.0359	-0.0959	-0.3343	0.1744	0.1362	-0.2229	-0.0167	0.0252	-0.1564	0.0035	-0.1645	55.735	21.22	58.973
4	5.4022	-0.0753	0.3055	4.0564	0.6454	4.6985	0.1508	1.4732	-1.1865	-0.7797	-0.1385	0.4694	0.3923	-0.3831	-0.0123	0.1089	-0.0112	-0.0698	0.4555	-0.3849	0.1331	48.271	5.913	36.653
5	4.3067	-0.0551	0.6367	1.3817	0.5586	1.2991	-0.056	0.4369	-0.448	-0.2173	0.0371	-0.1431	0.0404	0.1639	0.0189	-0.1611	-0.015	0.0478	-0.0663	-0.0522	-0.097	61.493	14.122	54.139
6	1.0438	-2.2413	-0.5305	11.1148	3.3759	1.0635	-0.2266	-0.4955	0.1314	0.6175	0.4005	-0.6292	0.013	0.1345	-0.1739	-0.0772	0.0049	-0.0103	-0.0382	0.0166	-0.0939	41.681	23.914	74.208
7	2.0584	-0.6838	-0.0338	3.9913	1.1778	3.3973	-0.1577	-0.1914	0.3885	0.2081	0.0999	-0.0943	-0.4907	0.1526	0.0578	-0.0255	-0.046	-0.0356	-0.1549	-0.098	-0.0788	59.558	45.952	98.231
8	2.2522	-1.0321	1.0474	3.563	-1.2837	2.5641	-0.0284	-0.0095	0.0199	-0.1284	-0.0257	0.2334	-0.105	-0.184	0.0542	-0.0952	-0.0323	0.0103	-0.1845	-0.0845	-0.0992	53.499	36.409	87.82
9	3.7415	1.0492	1.1949	9.9429	4.4674	5.4475	0.111	-0.1481	-0.2961	0.1723	-0.1614	0.3997	0.2061	-0.4364	0.0505	-0.05	-0.0404	0.0276	-0.1707	0.0042	-0.0393	53.988	21.47	97.391
10	3.765	-0.4111	1.4625	5.971	-0.2579	6.7474	-0.0049	-1.105	0.1265	1.7073	0.0526	-1.1991	-0.2162	0.4499	-0.0477	0.6576	-0.0425	-0.3626	0.282	-0.0239	0.1914	69.34	28.908	119.696
11	1.9624	0.4635	1.2725	5.602	-0.1192	3.1994	0.1864	-0.3063	-0.6257	0.759	-0.0678	-0.2154	0.4803	-0.0062	-0.1186	0.1446	-0.0284	-0.0556	-0.1225	0.0296	0.1026	59.61	15.312	103.297
12	8.4604	-2.6316	4.4828	1.1309	-1.2533	2.4389	0.3438	0.5227	-0.4767	-0.5952	-0.1232	0.1774	0.2371	0.1189	-0.2206	0.0062	-0.0213	0.0055	-0.0833	-0.0912	-0.0194	55.044	34.298	80.518
13	5.7958	-0.1199	-0.7298	18.6455	12.2641	8.1399	0.0626	0.9771	-0.6689	-0.1452	0.0976	-0.1879	0.2993	-0.0511	-0.1602	-0.1422	-0.0247	-0.0056	-0.0526	-0.12	-0.0943	44.441	12.453	50.504
14	0.6231	-2.5594	0.4639	10.5134	-1.9056	0.3454	-0.1972	-0.0215	0.0323	0.9024	-0.0349	-0.7483	-0.1608	0.1474	0.2321	0.0036	-0.0387	-0.0431	-0.0405	-0.0553	-0.0757	64.157	32.147	105.125
15	0.3894	0.078	0.2757	0.2754	0.1938	0.7963	-0.0204	0.0154	0.0065	0.0148	0.0228	-0.0002	-0.0187	-0.0073	-0.0024	-0.0417	-0.0171	0.0149	-0.0588	0.0047	0.0145	50.4409	25.1767	71.0363

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	A	A	5 - 99	1 - 95
2	2	A	A	100 - 146	96 - 142
3	3	A	A	147 - 181	143 - 177
4	4	A	A	182 - 261	178 - 257
5	5	A	A	262 - 338	258 - 334
6	6	A	A	339 - 375	335 - 371
7	7	B	B	5 - 99	1 - 95
8	8	B	B	100 - 146	96 - 142
9	9	B	B	147 - 181	143 - 177
10	10	B	B	182 - 261	178 - 257
11	11	B	B	262 - 338	258 - 334
12	12	B	B	339 - 375	335 - 371
13	13	A	C	1401	1
14	14	B	D	1501	1
15	15	A	G	1403 - 1671	1 - 269

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