PDB-9axb: Structure of Gp54 from Escherichia phage Bas11

ID or keywords:

Entry

Database: PDB / ID: 9axb

Title

Structure of Gp54 from Escherichia phage Bas11

Components

Gp54

Keywords

VIRAL PROTEIN / phage protein

Biological species

Escherichia phage JohannLBurckhardt (virus)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Zhang, T. / Lim, D.C. / Laub, M.T.

Funding support

United States, 1items

Citation

Journal: Nature / Year: 2024
Title: A bacterial immunity protein directly senses two disparate phage proteins.
Authors: Zhang, T. / Cepauskas, A. / Nadieina, A. / Thureau, A. / Coppieters 't Wallant, K. / Martens, C. / Lim, D.C. / Garcia-Pino, A. / Laub, M.T.

History

Deposition	Mar 6, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 20, 2024	Provider: repository / Type: Initial release
Revision 1.1	Dec 4, 2024	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9axb.cif.gz	238.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9axb.ent.gz	197.6 KB	Display	PDB format
PDBx/mmJSON format	9axb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9axb_validation.pdf.gz	457.6 KB	Display	wwPDB validaton report
Full document	9axb_full_validation.pdf.gz	459.4 KB	Display
Data in XML	9axb_validation.xml.gz	18.5 KB	Display
Data in CIF	9axb_validation.cif.gz	24.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ax/9axb ftp://data.pdbj.org/pub/pdb/validation_reports/ax/9axb	HTTPS FTP

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Related structure data

Related structure data	9ervC C: citing same article (ref.)

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Gp54

B: Gp54

C: Gp54

D: Gp54

E: Gp54

F: Gp54

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

1

A: Gp54

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

2

B: Gp54

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

3

C: Gp54

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

4

D: Gp54

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

5

E: Gp54

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

6

F: Gp54

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

Unit cell

Length a, b, c (Å)	50.000, 54.630, 54.590
Angle α, β, γ (deg.)	78.54, 78.83, 69.88
Int Tables number	1
Space group name H-M	P1

#1: Protein	Gp54 Mass: 8971.309 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia phage JohannLBurckhardt (virus) Production host: Escherichia coli (E. coli)
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.53 Å³/Da / Density % sol: 51.3 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 3.2 M potassium acetate pH 7.0

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5406 Å

Detector

Type: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 18, 2023 / Details: Osmic VariMax HF

Radiation

Monochromator: Osmic VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5406 Å / Relative weight: 1

Reflection

Resolution: 1.99→24.29 Å / Num. obs: 26616 / % possible obs: 73.1 % / Redundancy: 2 % / CC_1/2: 0.994 / R_merge(I) obs: 0.074 / R_rim(I) all: 0.104 / Net I/σ(I): 6.91

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
1.99-2.11	0.91	1253	0.405	1.288	1
2.11-2.25	0.599	2583	0.7	0.848	1
2.25-2.43	0.404	4402	0.826	0.571	1
2.43-2.66	0.281	4421	0.903	0.397	1
2.66-2.97	0.156	3952	0.956	0.221	1
2.97-3.43	0.07	3510	0.99	0.099	1
3.43-4.19	0.042	2969	0.994	0.059	1
4.19-5.9	0.037	2267	0.995	0.053	1
5.9-24.29	0.036	1259	0.995	0.051	1

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
XDS		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.3→24.29 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.55 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2518	3542	9.25 %	random
R_work	0.2112	-	-	-
obs	0.2151	21636	81.87 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.3→24.29 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3101	0	0	135	3236

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	3166
X-RAY DIFFRACTION	f_angle_d	0.478	4293
X-RAY DIFFRACTION	f_dihedral_angle_d	12.866	1183
X-RAY DIFFRACTION	f_chiral_restr	0.045	507
X-RAY DIFFRACTION	f_plane_restr	0.003	533

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.3-2.33	0.3765	119	0.2826	1171	X-RAY DIFFRACTION	71
2.33-2.36	0.3313	140	0.2833	1360	X-RAY DIFFRACTION	77
2.36-2.4	0.3818	130	0.2783	1345	X-RAY DIFFRACTION	80
2.4-2.44	0.2959	134	0.2832	1332	X-RAY DIFFRACTION	79
2.44-2.48	0.3148	141	0.2771	1391	X-RAY DIFFRACTION	79
2.48-2.52	0.3511	132	0.2908	1348	X-RAY DIFFRACTION	81
2.52-2.57	0.4072	141	0.2864	1373	X-RAY DIFFRACTION	81
2.57-2.61	0.3841	150	0.2686	1396	X-RAY DIFFRACTION	80
2.62-2.67	0.3188	130	0.2844	1330	X-RAY DIFFRACTION	81
2.67-2.73	0.3372	139	0.2632	1414	X-RAY DIFFRACTION	80
2.73-2.79	0.2872	134	0.2696	1339	X-RAY DIFFRACTION	82
2.79-2.86	0.3493	142	0.2787	1398	X-RAY DIFFRACTION	82
2.86-2.94	0.2936	141	0.2799	1374	X-RAY DIFFRACTION	82
2.94-3.02	0.2916	148	0.2612	1417	X-RAY DIFFRACTION	82
3.02-3.12	0.304	141	0.2342	1361	X-RAY DIFFRACTION	82
3.12-3.23	0.2622	143	0.2286	1391	X-RAY DIFFRACTION	82
3.23-3.36	0.2236	151	0.2071	1454	X-RAY DIFFRACTION	84
3.36-3.51	0.24	142	0.1868	1401	X-RAY DIFFRACTION	83
3.51-3.7	0.2834	145	0.2018	1434	X-RAY DIFFRACTION	84
3.7-3.93	0.2388	153	0.1712	1423	X-RAY DIFFRACTION	85
3.93-4.23	0.1777	149	0.1452	1444	X-RAY DIFFRACTION	84
4.23-4.65	0.1712	143	0.1452	1402	X-RAY DIFFRACTION	84
4.65-5.32	0.1918	152	0.1612	1484	X-RAY DIFFRACTION	86
5.32-6.67	0.2398	149	0.202	1472	X-RAY DIFFRACTION	87
6.68-24.29	0.1852	153	0.2068	1489	X-RAY DIFFRACTION	88

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	3.2288	-3.3019	-3.0106	4.1207	2.8862	8.1786	0.482	0.5362	0.7739	-0.2224	-0.2586	0.3123	-0.9526	-0.2334	0.1463	0.4258	-0.0802	-0.0688	0.2627	0.0078	0.2966	0.6699	5.5749	1.8815
2	5.0307	-1.6597	-1.502	4.0181	2.2	6.9976	0.0869	0.2744	-0.1919	-0.0272	-0.2876	0.2965	0.1631	-0.5717	0.3475	0.2679	-0.0945	-0.0301	0.2919	-0.001	0.252	1.3019	-1.1229	-2.4716
3	6.7924	2.4862	3.3752	6.1223	2.1545	8.6332	0.122	0.3732	-0.1036	0.0417	0.0526	0.7888	-0.0088	0.3471	-0.08	0.259	-0.0596	0.0312	0.3575	0.0091	0.3612	-2.5689	-4.2031	1.4816
4	5.2058	-1.6687	-1.0444	9.0903	2.1419	3.2127	-0.2551	-0.0948	-0.0762	0.1902	0.4401	0.5684	0.1488	-0.3671	-0.053	0.3626	-0.0697	0.0007	0.3357	0.0403	0.2362	6.3214	1.0702	4.4895
5	0.6979	-1.1168	-0.8647	2.7546	2.02	1.5051	-0.2019	-0.2115	-0.4737	-0.2001	0.3803	0.0661	0.0714	1.1151	-0.1597	0.395	0.1234	0.0624	0.5626	0.1086	0.3384	25.0121	1.2892	4.3913
6	4.128	-2.5462	-1.2933	7.9689	3.0588	8.401	-0.0962	-0.3905	-0.0729	0.2204	-0.0275	0.0137	-0.5601	0.5532	0.0987	0.3404	-0.0816	-0.0401	0.2878	0.0064	0.2797	19.5229	16.454	9.2743
7	3.5704	4.6896	-4.2763	6.8622	-5.1344	5.6026	-0.528	-0.2618	-0.108	0.541	-0.0803	-1.7038	0.7131	0.4308	0.8874	0.3467	0.0744	-0.0643	0.4164	-0.0024	0.5404	27.6719	0.3002	10.5872
8	6.5453	4.5885	0.5508	3.7492	-1.4322	5.8957	0.2263	-0.6407	-0.0733	-0.1811	-0.5817	-0.5495	-0.1127	0.5679	0.4454	0.3244	0.0698	-0.0655	0.4201	-0.0168	0.4025	25.4778	6.1909	14.2044
9	4.9812	-2.2734	-0.0497	2.6306	1.4303	6.632	-0.2127	-0.5023	-0.1909	-0.0732	0.0542	0.1696	0.3332	0.3757	0.0792	0.3158	-0.0728	-0.0171	0.2719	0.0434	0.2358	17.1248	3.3946	7.9991
10	6.1789	5.4673	-1.9292	7.896	-0.4446	1.2046	-0.1782	-0.6158	0.521	0.0692	-0.2619	0.2711	-0.4207	0.1617	0.0296	0.4363	0.0154	-0.1095	0.4319	-0.0666	0.2519	18.6276	10.2164	34.1682
11	8.1556	0.198	0.1095	7.943	-0.1994	6.2633	-0.1179	-0.0885	0.8322	-0.0555	0.4083	-0.514	-1.7552	1.19	0.1268	0.6602	-0.275	-0.1122	0.5018	0.0201	0.4387	26.399	17.957	25.5389
12	7.0991	-1.6962	0.7384	4.5327	3.9101	5.3753	-0.2623	-0.0991	-0.3412	0.7598	0.2704	0.2911	0.1723	-0.3077	0.1425	0.4275	0.0041	0.0429	0.6331	0.0776	0.2386	13.4553	5.9459	29.5486
13	1.7282	0.2382	1.74	2.7378	-2.6613	7.1106	-0.3672	-0.0247	-0.0474	0.0866	0.2215	-0.1514	-0.3524	-0.5908	0.0572	0.4243	-0.0287	0.0014	0.449	-0.0037	0.2454	21.0335	7.5493	28.1885
14	3.6757	0.1571	-3.4383	3.7424	3.9558	7.8136	0.8863	0.0588	0.0396	-0.4007	-0.4971	1.1494	-0.7842	-1.0623	-0.4317	0.4277	0.0576	0.046	0.4068	0.0301	0.5643	-3.4317	27.3475	4.4002
15	2.7885	-0.599	0.1112	8.4276	0.4501	3.3454	0.0639	-0.3448	0.4187	0.4332	-0.434	0.2693	-0.3743	-0.6488	0.0067	0.245	-0.0178	0.0298	0.2809	-0.0288	0.3436	0.9705	14.948	9.2076
16	4.8318	1.483	1.8144	2.5498	1.4664	5.9712	0.1692	-0.5418	0.9173	0.0625	-0.8079	1.5586	-1.1284	-0.3959	0.4576	0.4557	0.2445	0.059	0.3745	0.1022	0.8859	-7.4905	30.7464	10.8855
17	8.1591	5.6159	-0.6284	4.0082	-1.8419	7.6871	0.0209	0.0487	0.7381	0.6065	-0.2208	0.7411	-0.7598	-0.9105	0.3216	0.4011	0.01	0.1651	0.4086	-0.08	0.6878	-5.2313	24.9321	14.218
18	3.9419	-2.724	1.5737	6.67	-3.7029	8.6641	-0.2219	-0.37	0.2153	0.5098	0.4106	0.464	-0.6095	-0.2859	-0.1977	0.3213	-0.0047	0.0471	0.3027	-0.0283	0.3482	3.1624	27.8947	8.3072
19	7.7084	-3.2343	5.1142	4.3373	-1.4268	9.5694	0.3114	0.2898	-0.0071	-0.2776	-0.338	-0.1472	0.4061	0.4633	0.1924	0.3166	-0.1189	0.0324	0.2192	0.0278	0.3337	19.842	25.9467	1.9617
20	8.7946	-7.3006	1.7479	8.521	-2.8738	6.2643	0.1831	0.5293	0.3928	-1.2761	-0.0929	0.1708	-0.1656	-0.1561	0.1545	0.5372	-0.0567	-0.0182	0.408	0.0314	0.3194	14.8571	34.0818	-8.2936
21	5.4364	1.5965	0.8775	4.4879	4.4957	4.6013	-0.2044	-0.1353	0.251	0.1874	-0.3744	-0.1259	0.3445	0.3899	0.4143	0.5108	-0.062	0.0478	0.2875	0.0602	0.3983	25.075	30.3248	6.1951
22	5.7553	3.4013	-4.818	5.5096	-3.8611	4.3063	-0.1767	-0.1256	-0.0017	-0.1616	-0.0037	-0.3369	0.139	0.1507	-0.0371	0.4424	-0.0053	-0.0607	0.2849	0.0099	0.3186	22.9175	35.5097	1.7404
23	0.8876	0.8971	-1.3301	6.3103	-1.7816	2.8324	0.0586	0.0745	0.0667	0.102	0.1717	0.3641	-0.4029	0.0705	-0.2153	0.2952	-0.0752	-0.0155	0.2942	-0.0242	0.202	14.0295	30.3352	4.5765
24	8.7119	-1.686	-6.5103	5.0123	1.6454	5.1327	0.2026	-0.2853	-0.2469	0.1378	-0.1622	-0.9719	-0.2674	1.6552	0.036	0.4796	0.0105	-0.0673	0.8672	-0.0797	0.476	30.5536	-3.2473	-15.6816
25	5.571	-1.0839	-3.4602	7.2386	-2.4085	8.0763	-0.0468	0.132	-0.3697	0.3992	0.3448	-0.1022	0.7907	0.6019	-0.2177	0.4431	0.006	-0.0803	0.4478	-0.0009	0.2556	23.5518	-4.8437	-3.6019
26	4.7286	1.7969	1.2593	6.5796	1.1384	5.9572	-0.1035	1.0346	-0.5117	0.362	0.1316	-0.4325	1.4702	1.4803	-0.4125	0.6921	0.3704	-0.088	0.9356	-0.1607	0.4112	31.7588	-11.9749	-13.7254
27	8.8812	0.0994	-2.6182	6.2388	-0.2297	2.0774	0.0603	0.5273	-0.6764	-0.5081	0.0049	-0.4604	0.2732	0.691	0.1039	0.4291	0.0003	-0.0052	0.4892	-0.0708	0.2671	23.3919	-6.3459	-16.6192

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 11 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 12 through 34 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 35 through 47 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 48 through 66 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1 through 11 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 12 through 25 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 26 through 34 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 35 through 47 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 48 through 66 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 3 through 11 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 12 through 25 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 26 through 34 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 35 through 66 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 3 through 11 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 12 through 25 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 26 through 34 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 35 through 47 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 48 through 66 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 3 through 11 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 12 through 25 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 26 through 34 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 35 through 47 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 48 through 66 )
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 3 through 11 )
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 12 through 25 )
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 26 through 47 )
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 48 through 66 )

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-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
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

-
Yorodumi