PDB-2xf7: Crystal structure of Bacillus subtilis SPP1 phage gp23.1, a putat...

ID or keywords:

Entry

Database: PDB / ID: 2xf7

Title

Crystal structure of Bacillus subtilis SPP1 phage gp23.1, a putative chaperone. High-resolution structure.

Components

GP23.1

Keywords

VIRAL PROTEIN

Function / homology

Arc Repressor Mutant, subunit A - #1530 / : / SPP1 phage GP23.1 / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / Bacteriophage SPP1 complete nucleotide sequence

Function and homology information

Biological species

BACILLUS PHAGE SPP1 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.61 Å

Authors

Veesler, D. / Blangy, S. / Lichiere, J. / Ortiz-Lombardia, M. / Tavares, P. / Campanacci, V. / Cambillau, C.

Citation

Journal: Protein Sci. / Year: 2010
Title: Crystal Structure of Bacillus Subtilis Spp1 Phage Gp23.1, A Putative Chaperone.
Authors: Veesler, D. / Blangy, S. / Lichiere, J. / Ortiz-Lombardia, M. / Tavares, P. / Campanacci, V. / Cambillau, C.

History

Deposition	May 20, 2010	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 11, 2010	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2xf7.cif.gz	134.2 KB	Display	PDBx/mmCIF format
PDB format	pdb2xf7.ent.gz	107.9 KB	Display	PDB format
PDBx/mmJSON format	2xf7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2xf7_validation.pdf.gz	464.2 KB	Display	wwPDB validaton report
Full document	2xf7_full_validation.pdf.gz	466.2 KB	Display
Data in XML	2xf7_validation.xml.gz	15.6 KB	Display
Data in CIF	2xf7_validation.cif.gz	23.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xf/2xf7 ftp://data.pdbj.org/pub/pdb/validation_reports/xf/2xf7	HTTPS FTP

-
Related structure data

Related structure data	2xf5SC 2xf6C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2xf5-d 2xf6-1 2yms-d 6tji-1 6tje-d 1yav-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: GP23.1

B: GP23.1

C: GP23.1

D: GP23.1

E: GP23.1

F: GP23.1

34.1 kDa, 6 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)	52.427, 66.902, 82.433
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	GP23.1 Mass: 5687.134 Da / Num. of mol.: 6 / Fragment: RESIDUES 2-51 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS PHAGE SPP1 (virus) / Plasmid: PETG20A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): T7 EXPRESS IQ PLYSS / References: UniProt: O48468
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 1.92 Å³/Da / Density % sol: 35.49 % / Description: NONE
Crystal grow	Details: 0.2M NASCN, 2.2M (NH4)2SO4

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97372
Detector	Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 4, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97372 Å / Relative weight: 1
Reflection	Resolution: 1.61→41.27 Å / Num. obs: 37993 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / B_iso Wilson estimate: 18.15 Å² / R_merge(I) obs: 0.06 / Net I/σ(I): 21.4
Reflection shell	Resolution: 1.61→1.7 Å / Redundancy: 4.6 % / R_merge(I) obs: 0.42 / Mean I/σ(I) obs: 3.3 / % possible all: 90.6

-
Processing

Software

Name	Version	Classification
BUSTER-TNT	2.9.2	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XF5

2xf5

Resolution: 1.61→22.73 Å / Cor.coef. F_o:F_c: 0.9598 / Cor.coef. F_o:F_c free: 0.9481 / Cross valid method: THROUGHOUT / σ(F): 0

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2008	1324	3.55 %	RANDOM
R_work	0.1684	-	-	-
obs	0.1696	37265	-	-

Displacement parameters

B_iso mean: 23.34 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.2888 Å²	0 Å²	0 Å²
2-	-	-2.0406 Å²	0 Å²
3-	-	-	1.7517 Å²

Refine analyze

Luzzati coordinate error obs: 0.197 Å

Refinement step

Cycle: LAST / Resolution: 1.61→22.73 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2300	0	0	320	2620

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.014	2438	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.11	3340	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		811	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes		72	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes		357	HARMONIC	5
X-RAY DIFFRACTION	t_it		2438	HARMONIC	20
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_omega_torsion	3.32
X-RAY DIFFRACTION	t_other_torsion	15.69
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		295	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact		3252	SEMIHARMONIC	4

LS refinement shell

Resolution: 1.61→1.65 Å / Total num. of bins used: 19

	R_factor	Num. reflection	% reflection
R_free	0.1991	82	3.81 %
R_work	0.1893	2071	-
all	0.1897	2153	-

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	0.7429	0.7333	-0.5705	3.3718	0.7485	4.831	0.0005	-0.0677	-0.0066	0.0221	0.0441	-0.0211	0.0008	-0.3308	-0.0445	-0.1126	-0.0116	0.0007	0.1079	0.0187	-0.0997	-18.2735	9.6931	-25.2102
2	2.6763	-0.6841	-0.3672	4.8144	0.0207	0.7964	-0.0548	0.4262	0.0476	-0.0552	0.2208	0.1878	0.0383	-0.543	-0.166	-0.2046	-0.0201	-0.0002	0.2888	0.0517	-0.1814	-28.8906	10.9117	-23.1654
3	1.114	0.5628	-1.9197	2.5207	2.0373	7.8824	-0.0049	0.1728	-0.0823	-0.1304	0.0843	0.1235	0.0685	-0.9158	-0.0794	-0.1057	0.0033	-0.0092	0.1628	0.029	-0.1191	-21.5026	11.2639	-30.9411
4	1.6533	-0.1123	-0.5436	5.5598	-0.9265	3.0196	-0.025	0.043	0.0284	-0.1656	-0.0219	-0.2429	-0.1006	0.2676	0.047	-0.0897	0.0046	0.0086	0.0871	0.0222	-0.044	-7.0346	6.1138	-4.4569
5	2.4843	0.5235	-0.6795	5.4941	-0.1641	1.9637	-0.1225	-0.3417	0.0276	0.064	-0.029	-0.2865	-0.0828	0.0854	0.1515	-0.076	0.0001	0.0065	0.1292	0.0141	-0.0331	0.0464	4.7533	3.1513
6	0.7159	-0.7086	-0.3023	1.7661	0.5529	1.2171	-0.0279	-0.1358	-0.0298	-0.0102	0.0092	0.1022	0.0489	0.0028	0.0187	-0.0571	0.0148	-0.0026	0.0703	0.0226	-0.0275	-10.7326	4.7327	1.2763
7	3.8448	-0.3164	0.1443	1.9349	1.2856	3.3595	0.1624	-0.1348	-0.1052	0.086	-0.0522	-0.0316	-0.0164	-0.0621	-0.1103	-0.0839	-0.024	-0.0128	0.0534	0.0089	-0.0573	-6.0031	11.412	-31.891
8	3.3232	-0.8871	0.5794	4.3299	0.4283	1.3526	0.0573	0.0706	-0.1473	-0.1071	0.0282	0.0691	-0.0413	-0.1427	-0.0855	-0.011	-0.0025	-0.0014	0.0893	0.0139	-0.0662	-13.2999	13.5716	-39.204
9	5.8051	-2.0149	0.5353	2.4712	1.5194	3.6495	0.1538	0.4939	-0.1944	-0.1004	-0.044	0.0655	-0.1068	0.3573	-0.1098	-0.0539	-0.029	-0.0071	0.0984	-0.0259	-0.0589	-2.5356	12.8102	-37.8106
10	4.6037	0.257	-0.0026	1.2347	0.8604	4.6979	-0.0361	0.0123	-0.119	-0.0442	-0.0805	0.0028	0.1241	-0.172	0.1166	-0.0648	-0.037	0.0022	0.1123	-0.0043	-0.062	5.7205	9.8501	-24.809
11	3.3657	1.1926	0.0925	2.9664	-1.2832	4.9269	-0.0485	0.1536	-0.027	-0.209	-0.0035	-0.1851	0.0418	0.4301	0.052	-0.0954	-0.0313	0.0071	0.0971	-0.0043	-0.0941	9.4864	12.6637	-34.509
12	4.28	-2.0184	1.278	3.888	-1.0487	4.8807	0.0427	-0.0588	-0.2375	-0.0283	-0.0896	-0.0337	0.2349	0.3831	0.0469	-0.0913	-0.0159	0.0055	0.1201	-0.0093	-0.052	12.7641	9.6585	-24.3904
13	4.2514	-0.4732	-1.7405	4.8961	0.5934	4.5486	-0.1072	0.3709	-0.2724	-0.0395	-0.1718	0.1514	0.1005	-0.0319	0.2789	-0.0929	-0.0222	0.0192	0.1203	-0.0281	-0.0319	4.9062	6.7989	-11.1132
14	3.2862	-2.0204	1.9741	3.48	1.3631	3.5084	0.0335	0.1646	-0.1309	0.0493	-0.2275	-0.1306	0.09	0.7823	0.194	-0.1476	-0.019	0.0194	0.2432	0.0584	-0.1062	15.2401	7.8511	-13.1231
15	4.3441	2.2731	-2.3385	7.6732	-2.5574	5.201	-0.217	-0.0991	-0.3112	0.1337	-0.0666	-0.0194	0.3006	0.3273	0.2836	-0.099	0.0048	0.0293	0.0802	0.002	-0.0832	8.265	5.3199	-5.1965
16	5.0218	-0.0886	-1.1794	3.311	-2.0993	6.818	-0.029	0.2577	-0.0217	-0.248	-0.0354	0.0049	0.233	-0.3181	0.0644	-0.0907	0.0135	-0.0135	0.0976	0.0097	-0.0915	-18.9024	8.0563	-11.6765
17	4.458	1.1959	-1.084	5.4445	0.3223	5.0348	0.0289	-0.2519	-0.0352	0.1808	0.0291	0.2225	0.147	-0.2431	-0.0579	-0.1201	0.025	-0.0064	0.072	0.0297	-0.0954	-21.931	6.3187	-1.3928
18	4.0627	1.4363	0.8309	2.4791	-2.2314	6.4565	0.0803	0.6231	0.037	-0.0502	0.4784	0.0433	0.2278	-1.059	-0.5587	-0.1287	-0.0016	-0.0314	0.3001	0.0426	-0.0894	-25.9758	8.2694	-11.3822

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(A3-18)
2	X-RAY DIFFRACTION	2	(A19-32)
3	X-RAY DIFFRACTION	3	(A33-50)
4	X-RAY DIFFRACTION	4	(B2-18)
5	X-RAY DIFFRACTION	5	(B19-32)
6	X-RAY DIFFRACTION	6	(B33-50)
7	X-RAY DIFFRACTION	7	(C3-18)
8	X-RAY DIFFRACTION	8	(C19-32)
9	X-RAY DIFFRACTION	9	(C33-50)
10	X-RAY DIFFRACTION	10	(D3-18)
11	X-RAY DIFFRACTION	11	(D19-32)
12	X-RAY DIFFRACTION	12	(D33-50)
13	X-RAY DIFFRACTION	13	(E3-18)
14	X-RAY DIFFRACTION	14	(E19-32)
15	X-RAY DIFFRACTION	15	(E33-50)
16	X-RAY DIFFRACTION	16	(F2-18)
17	X-RAY DIFFRACTION	17	(F19-32)
18	X-RAY DIFFRACTION	18	(F33-49)

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and 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

-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

-
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