PDB-5boi: Bacillus megaterium YpeB C-terminal domain

ID or keywords:

Entry

Database: PDB / ID: 5boi

Title

Bacillus megaterium YpeB C-terminal domain

Components

Germination protein YpeB

Keywords

UNKNOWN FUNCTION / PepSY domain / inhibitory protein

Function / homology

Spore germination YpeB / : / YpeB sporulation, PepSY1 and PepSY2 domains / YpeB N-terminal / spore germination / PepSY domain / Peptidase propeptide and YPEB domain / Germination protein YpeB

Function and homology information

Biological species

Bacillus megaterium QM B1551 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / AB INITIO PHASING / Resolution: 1.8 Å

Authors

Christie, G. / Chirgadze, D.Y. / Ustok, F.I.

Citation

Journal: Proteins / Year: 2015
Title: Crystal structure of the PepSY-containing domain of the YpeB protein involved in germination of bacillus spores.
Authors: Ustok, F.I. / Chirgadze, D.Y. / Christie, G.

History

Deposition	May 27, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Aug 12, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 16, 2015	Group: Database references
Revision 1.2	May 8, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5boi.cif.gz	109.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5boi.ent.gz	85.1 KB	Display	PDB format
PDBx/mmJSON format	5boi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5boi_validation.pdf.gz	442.8 KB	Display	wwPDB validaton report
Full document	5boi_full_validation.pdf.gz	446.2 KB	Display
Data in XML	5boi_validation.xml.gz	11.7 KB	Display
Data in CIF	5boi_validation.cif.gz	15.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bo/5boi ftp://data.pdbj.org/pub/pdb/validation_reports/bo/5boi	HTTPS FTP

-
Related structure data

Similar structure data	3t9k-2 3t9k-1 1xtn-d 5fq3-4 1zgw-d 5fq3-2 6x9n-4 3jue-2 6ieo-d 1rz5-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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Germination protein YpeB

hetero molecules

28.4 kDa, 1 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)	53.208, 110.104, 85.806
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-655- HOH
2	1	A-700- HOH

#1: Protein	Germination protein YpeB Mass: 28205.895 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus megaterium QM B1551 (bacteria) Gene: ypeB, BMQ_4349 / Plasmid: pBADcLIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Top10 / References: UniProt: D5DRI0
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 2.34 Å³/Da / Density % sol: 47.5 % / Description: thin plate-type
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.27 M lithium sulphate, 44 % (v/v) PEG 400, 0.1 M sodium acetate

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 2, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.8→47.91 Å / Num. obs: 23741 / % possible obs: 99.9 % / Redundancy: 7.3 % / R_merge(I) obs: 0.06 / R_sym value: 0.06 / Net I/σ(I): 15.7
Reflection shell	Resolution: 1.8→1.9 Å / Redundancy: 7.5 % / R_merge(I) obs: 0.84 / Mean I/σ(I) obs: 2.5 / % possible all: 99.9

-
Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure: AB INITIO PHASING / Resolution: 1.8→46.34 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.44 / Phase error: 25.01 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2265	1997	8.43 %
R_work	0.1953	-	-
obs	0.198	23700	99.76 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.8→46.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1810	0	10	100	1920

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	1871
X-RAY DIFFRACTION	f_angle_d	1.109	2522
X-RAY DIFFRACTION	f_dihedral_angle_d	14.613	716
X-RAY DIFFRACTION	f_chiral_restr	0.049	281
X-RAY DIFFRACTION	f_plane_restr	0.005	326

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 (%)
1.8-1.845	0.2982	138	0.2989	1528	X-RAY DIFFRACTION	100
1.845-1.8949	0.2803	141	0.2524	1510	X-RAY DIFFRACTION	100
1.8949-1.9507	0.2647	140	0.2285	1526	X-RAY DIFFRACTION	99
1.9507-2.0137	0.249	139	0.2082	1510	X-RAY DIFFRACTION	100
2.0137-2.0856	0.2487	142	0.188	1540	X-RAY DIFFRACTION	100
2.0856-2.1691	0.2684	141	0.197	1541	X-RAY DIFFRACTION	100
2.1691-2.2679	0.2671	142	0.1934	1546	X-RAY DIFFRACTION	100
2.2679-2.3874	0.2367	142	0.2	1536	X-RAY DIFFRACTION	100
2.3874-2.537	0.2444	143	0.2121	1557	X-RAY DIFFRACTION	100
2.537-2.7328	0.2673	142	0.2102	1541	X-RAY DIFFRACTION	100
2.7328-3.0078	0.2592	143	0.209	1552	X-RAY DIFFRACTION	100
3.0078-3.4429	0.216	146	0.1934	1571	X-RAY DIFFRACTION	100
3.4429-4.3372	0.1802	145	0.1687	1590	X-RAY DIFFRACTION	100
4.3372-46.3506	0.2114	153	0.1907	1655	X-RAY DIFFRACTION	100

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	0.237	0.05	-0.187	0.1048	-0.0954	0.1643	0.4309	-1.3622	0.4966	0.19	-0.2361	-0.0822	-0.7903	0.6678	-0.0198	0.7275	-0.1223	0.0884	0.9535	-0.2619	0.6804	59.3536	82.3064	38.0588
2	1.3001	0.0435	0.1009	0.1501	-0.122	2.862	-0.1648	-0.481	1.3108	0.5511	-0.1479	-0.4397	-1.3267	0.3501	-0.136	0.576	-0.1136	-0.0746	0.3065	0.0543	0.8597	59.9602	82.9567	29.4023
3	0.388	-0.5056	0.7069	2.4379	-0.4948	1.993	-0.6597	0.7167	0.9498	-0.0249	0.1238	-0.3512	-0.3895	0.6404	-0.9076	0.4722	-0.1495	0.0051	0.6292	-0.0828	0.6794	66.2592	75.7118	27.8792
4	0.8622	0.2503	0.3676	0.6943	0.0058	1.4447	0.0746	-0.5696	0.3429	-0.2878	0.0669	-0.1854	-0.2404	0.1101	-0.0058	0.2482	-0.0488	0.0426	0.2638	-0.0834	0.2714	60.3382	68.1776	29.2994
5	0.2557	-0.3745	-0.3049	0.271	0.535	0.6169	-0.454	-1.0086	-0.5532	0.6496	0.0885	0.5164	0.3674	0.6463	-0.0176	0.3009	-0.0464	0.0108	0.4424	-0.0428	0.2116	56.372	59.5417	38.2579
6	0.9126	-0.1673	0.1964	0.0509	-0.427	0.7274	-0.0736	-0.088	0.0415	0.0272	0.0708	0.0308	0.0096	0.2016	-0.0001	0.239	0.0036	0.0242	0.2542	-0.0421	0.2478	48.7057	61.9589	32.9482
7	1.9551	0.0019	-0.7519	0.4855	0.2415	1.9842	0.0215	-0.1016	0.1657	0.0081	-0.0057	0.1206	-0.0062	-0.0965	0.0002	0.2169	0.0282	-0.0046	0.1868	0.0174	0.2388	37.9103	58.6335	32.9171
8	1.1047	1.0715	-0.0541	1.6316	-0.0838	2.1773	-0.1101	0.507	0.0425	-0.0338	0.056	-0.1684	0.1068	-0.0218	-0.0002	0.2254	-0.0044	0.0114	0.2859	0.0074	0.2101	34.9803	53.8628	26.4524

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 216 through 232 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 233 through 259 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 260 through 272 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 273 through 293 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 294 through 308 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 309 through 349 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 350 through 401 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 402 through 441 )

-
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