PDB-3cdd: Crystal structure of prophage MuSo2, 43 kDa tail protein from She...

ID or keywords:

Entry

Database: PDB / ID: 3cdd

Title

Crystal structure of prophage MuSo2, 43 kDa tail protein from Shewanella oneidensis

Components

Prophage MuSo2, 43 kDa tail protein

Keywords

STRUCTURAL PROTEIN / MuSo2 / Shewanella oneidensis MR-1 /

Structural Genomics / PSI-2 /

Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

viral process
Similarity search - Function

Biological species

Shewanella oneidensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.1 Å

Authors

Chang, C. / Evdokimova, E. / Kudritska, M. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of prophage MuSo2, 43 kDa tail protein from Shewanella oneidensis.
Authors: Chang, C. / Evdokimova, E. / Savchenko, A. / Edwards, A.M. / Joachimiak, A.

History

Deposition	Feb 26, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 11, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3cdd.cif.gz	401.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3cdd.ent.gz	342.2 KB	Display	PDB format
PDBx/mmJSON format	3cdd.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/cd/3cdd ftp://data.pdbj.org/pub/pdb/validation_reports/cd/3cdd	HTTPS FTP

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Related structure data

Similar structure data	1wru-1 6u5h-d 3bpd-d 3gs9-1 3aqd-d 5jyx-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
Other databases	TargetDB: APC7502

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Prophage MuSo2, 43 kDa tail protein

B: Prophage MuSo2, 43 kDa tail protein

C: Prophage MuSo2, 43 kDa tail protein

D: Prophage MuSo2, 43 kDa tail protein

E: Prophage MuSo2, 43 kDa tail protein

F: Prophage MuSo2, 43 kDa tail protein

239 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Prophage MuSo2, 43 kDa tail protein

B: Prophage MuSo2, 43 kDa tail protein

C: Prophage MuSo2, 43 kDa tail protein

defined by author&software
119 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Prophage MuSo2, 43 kDa tail protein

E: Prophage MuSo2, 43 kDa tail protein

F: Prophage MuSo2, 43 kDa tail protein

defined by author&software
119 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	96.345, 82.445, 151.832
Angle α, β, γ (deg.)	90.00, 100.20, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Prophage MuSo2, 43 kDa tail protein Mass: 39798.117 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_2699 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8EDP4
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1090 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Prophage MuSo2, 43 kDa tail protein

Mass: 39798.117 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_2699 / Species (production host): Escherichia coli / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8EDP4

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 1090 / 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: 2.49 Å³/Da / Density % sol: 50.51 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2M KCl, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 24, 2007
Radiation	Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97929 Å / Relative weight: 1
Reflection	Resolution: 2.1→50 Å / Num. all: 137160 / Num. obs: 132747 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / B_iso Wilson estimate: 37.1 Å² / R_merge(I) obs: 0.072 / Net I/σ(I): 31.76
Reflection shell	Resolution: 2.1→2.18 Å / Redundancy: 5.1 % / R_merge(I) obs: 0.449 / Mean I/σ(I) obs: 2.53 / Num. unique all: 11129 / % possible all: 81.6

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.1→47.69 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.925 / SU B: 11.462 / SU ML: 0.16 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.224 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25664	6664	5 %	RANDOM
R_work	0.20112	-	-	-
all	0.20392	132662	-	-
obs	0.20392	132662	96.57 %	-

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: 34.017 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.34 Å²	0 Å²	0.17 Å²
2-	-	-2.16 Å²	0 Å²
3-	-	-	3.57 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→47.69 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14956	0	0	1090	16046

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	15425
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.312	1.955	20944
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.034	5	2014
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.441	24.235	647
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.776	15	2666
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.411	15	109
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	2420
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	11543
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.196	0.2	6736
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.298	0.2	10614
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.151	0.2	1137
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	0.184	0.2	115
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.191	0.2	25
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	0.659	1.5	10114
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.085	2	15845
X-RAY DIFFRACTION	r_scbond_it	1.76	3	6082
X-RAY DIFFRACTION	r_scangle_it	2.696	4.5	5079
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.1→2.15 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.315	399	-
R_work	0.243	7503	-
obs	-	7902	78.63 %

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	1.3774	-0.1636	-0.0234	2.9761	0.9655	0.8708	0.0593	-0.1798	-0.2613	0.3754	-0.1178	0.3499	0.1123	0.0966	0.0585	-0.1005	-0.0139	0.0199	-0.0804	0.0582	-0.1249	63.5381	-1.3958	45.6714
2	3.352	-1.1876	0.7167	4.4329	0.8398	1.4414	-0.1451	-0.0491	0.3655	0.1223	-0.0899	0.5852	-0.1532	-0.2361	0.235	-0.1232	0.036	0.056	-0.0716	-0.0321	0.1022	49.8558	26.637	44.8758
3	3.4314	-0.0743	-0.5774	3.0061	-0.5893	1.5989	0.2351	-0.4578	0.1891	0.4817	-0.1733	0.0052	-0.1172	0.2069	-0.0618	-0.0243	-0.107	-0.0177	-0.0328	-0.0155	-0.3161	78.1855	19.6344	50.5039
4	10.203	-4.4357	0.0048	11.7384	-2.0283	6.8887	-0.1153	-0.4519	0.1716	0.2028	0.4047	1.1053	-0.937	-1.3419	-0.2894	0.107	0.2438	0.0879	0.1645	0.0313	-0.1293	71.0741	39.3632	31.0884
5	4.733	1.2874	-0.5684	1.4465	-0.3728	0.892	0.005	0.2004	-0.3968	-0.4561	-0.0798	-0.0714	0.2392	0.0939	0.0748	0.0228	0.0901	-0.0176	-0.1441	-0.0294	-0.1481	76.5179	-6.4499	5.8166
6	4.7922	0.3983	-0.9829	2.6718	-1.3819	1.9167	0.0918	0.3766	0.502	-0.4018	0.0433	0.7346	-0.0377	-0.2859	-0.1351	-0.0534	0.0061	-0.2961	-0.083	0.0012	0.1987	48.1718	5.8428	2.7696
7	1.4178	-0.3259	0.5333	1.3394	-1.1686	3.3168	0.0889	-0.0899	-0.3105	-0.2246	0.0741	0.3748	0.338	-0.1305	-0.1629	-0.1727	-0.0229	-0.0806	-0.1683	0.0311	0.0452	58.2257	-13.4704	23.5016
8	4.5213	-0.9106	1.933	5.4122	1.179	7.4767	-0.1743	0.0672	0.1221	-0.5818	-0.0906	0.8211	-0.2907	-0.2869	0.2649	-0.2013	-0.0299	-0.1118	-0.1527	-0.0196	0.2265	42.11	10.1611	29.8908
9	1.8597	-0.218	-0.3626	1.3836	0.2703	3.0869	0.1123	-0.2327	-0.0577	0.0684	-0.0457	-0.5092	-0.0248	0.2459	-0.0666	-0.0549	-0.0289	0.0228	-0.0531	0.0234	-0.0125	93.7744	23.8035	29.6675
10	4.1718	-1.4379	-0.0635	4.4002	-0.7527	6.9395	0.1658	0.2786	0.4095	-0.7639	-0.2401	-0.0401	-0.8137	-0.5873	0.0743	0.2791	0.1824	0.0536	-0.0864	0.1141	-0.2232	79.1141	39.2183	8.7247
11	1.6284	0.2312	-0.7191	5.0641	0.9749	1.7275	0.0544	0.1688	-0.0363	-0.6332	0.2177	-0.4298	-0.1943	0.3013	-0.2722	-0.0198	0.0406	0.1481	-0.0053	-0.0206	-0.1512	92.8152	13.1385	6.2588
12	6.8139	-3.3293	2.1252	4.4809	-1.6779	0.8061	0.0003	0.0611	0.7236	0.1303	-0.1937	-0.1787	-0.0683	-0.1831	0.1934	0.136	0.0696	-0.1454	0.0587	0.0981	0.0332	63.9861	20.1571	-3.3374
13	1.1031	-0.3101	-0.4763	1.4329	-0.8445	3.9052	0.0383	-0.2225	-0.1059	0.0416	0.003	-0.259	-0.2018	0.2561	-0.0413	-0.0794	-0.0349	0.0002	0.0028	-0.0518	-0.1113	82.4894	24.1065	103.6475
14	3.8327	-1.4247	-0.9237	4.3828	-0.4009	9.6882	0.4004	0.3999	0.5211	-0.4577	0.0097	0.2273	-1.7481	-1.2208	-0.4101	0.3014	0.2898	0.068	-0.0154	0.1208	-0.068	66.0473	40.9848	84.4039
15	2.1857	0.0666	-1.6597	7.6741	0.8502	1.366	-0.0828	0.3841	-0.0805	-0.7239	0.251	0.0081	-0.156	0.22	-0.1682	-0.0034	0.0232	0.0808	0.0249	-0.0626	-0.1632	79.7546	15.2015	79.4024
16	6.0971	-2.7877	1.4481	3.4035	-1.0164	0.4029	-0.2263	0.0003	0.5545	0.1695	0.0477	-0.1247	-0.1866	-0.1025	0.1786	0.0454	0.0282	-0.1011	-0.0578	0.0244	0.0238	50.428	22.0726	71.4071
17	1.4537	-0.0864	-0.1913	2.9638	1.2407	1.2518	0.0761	-0.228	-0.1766	0.2294	-0.0801	0.2935	0.1791	0.0597	0.004	-0.1637	-0.0041	0.0235	-0.1304	0.0124	0.0375	52.8811	-1.5518	119.8753
18	2.4577	-1.343	0.3	2.4949	0.059	1.7351	0.0992	-0.0938	0.3575	0.1536	0.014	0.5495	-0.2074	-0.2361	-0.1132	-0.1493	0.0329	0.1504	-0.1191	-0.0595	0.3102	39.1103	26.4097	120.5898
19	4.1105	0.6754	-0.5822	2.2032	-1.1318	1.5447	0.2231	-0.4255	0.2901	0.277	-0.2084	0.2888	-0.07	0.2699	-0.0147	-0.1401	-0.0799	0.0188	-0.0489	-0.1102	-0.1913	67.737	19.1995	124.9233
20	9.0549	-4.9691	-2.8991	8.2439	-0.5506	9.189	-0.1398	-0.4581	-0.1016	0.3524	0.4725	1.0311	-1.3733	-1.3123	-0.3326	0.1237	0.3328	0.1415	0.1038	-0.0062	-0.0356	60.3314	39.561	107.1546
21	4.158	1.0799	-0.2438	1.5812	-0.0611	0.8272	-0.0617	0.1366	-0.3378	-0.3063	0.0525	0.0003	0.2268	0.102	0.0091	-0.0345	0.0511	-0.0276	-0.152	-0.0336	-0.0675	63.0021	-4.3882	78.5499
22	5.0308	1.5015	-1.1533	3.8533	-1.6462	2.2996	0.1566	0.4218	0.486	-0.2602	0.132	1.0132	-0.0346	-0.3649	-0.2886	-0.1495	-0.0029	-0.1663	-0.0692	0.0143	0.2822	35.1007	7.403	77.6933
23	1.0414	-0.2294	0.4786	1.4273	-0.4045	3.0091	0.0157	0.0077	-0.1136	-0.1147	0.0535	0.3078	0.4582	-0.1608	-0.0691	-0.1452	-0.0555	-0.0408	-0.2012	0.025	0.1106	46.4434	-12.6742	97.0488
24	5.642	0.196	2.1982	4.7771	-0.6894	4.9688	-0.1497	0.5286	0.2453	-0.6149	-0.0952	0.6401	0.0042	-0.3139	0.2449	-0.1896	0.0184	-0.1205	-0.0802	0.0019	0.3407	30.4127	10.9248	105.1257

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	2 - 95	4 - 97
2	X-RAY DIFFRACTION	2	A	A	96 - 180	98 - 182
3	X-RAY DIFFRACTION	3	A	A	181 - 204	183 - 206
4	X-RAY DIFFRACTION	3	A	A	279 - 341	281 - 343
5	X-RAY DIFFRACTION	4	A	A	205 - 278	207 - 280
6	X-RAY DIFFRACTION	5	B	B	3 - 95	5 - 97
7	X-RAY DIFFRACTION	6	B	B	96 - 180	98 - 182
8	X-RAY DIFFRACTION	7	B	B	181 - 204	183 - 206
9	X-RAY DIFFRACTION	7	B	B	279 - 341	281 - 343
10	X-RAY DIFFRACTION	8	B	B	205 - 278	207 - 280
11	X-RAY DIFFRACTION	9	C	C	3 - 95	5 - 97
12	X-RAY DIFFRACTION	10	C	C	96 - 180	98 - 182
13	X-RAY DIFFRACTION	11	C	C	181 - 204	183 - 206
14	X-RAY DIFFRACTION	11	C	C	279 - 341	281 - 343
15	X-RAY DIFFRACTION	12	C	C	205 - 278	207 - 280
16	X-RAY DIFFRACTION	13	D	D	2 - 95	4 - 97
17	X-RAY DIFFRACTION	14	D	D	96 - 180	98 - 182
18	X-RAY DIFFRACTION	15	D	D	181 - 204	183 - 206
19	X-RAY DIFFRACTION	15	D	D	279 - 341	281 - 343
20	X-RAY DIFFRACTION	16	D	D	205 - 278	207 - 280
21	X-RAY DIFFRACTION	17	E	E	1 - 95	3 - 97
22	X-RAY DIFFRACTION	18	E	E	96 - 180	98 - 182
23	X-RAY DIFFRACTION	19	E	E	181 - 204	183 - 206
24	X-RAY DIFFRACTION	19	E	E	279 - 341	281 - 343
25	X-RAY DIFFRACTION	20	E	E	205 - 278	207 - 280
26	X-RAY DIFFRACTION	21	F	F	3 - 95	5 - 97
27	X-RAY DIFFRACTION	22	F	F	96 - 180	98 - 182
28	X-RAY DIFFRACTION	23	F	F	181 - 204	183 - 206
29	X-RAY DIFFRACTION	23	F	F	279 - 341	281 - 343
30	X-RAY DIFFRACTION	24	F	F	205 - 278	207 - 280

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