PDB-8p8e: Crystal structure of endolysin gp46 from Pseudomonas aeruginosa b...

ID or keywords:

Entry

Database: PDB / ID: 8p8e

Title

Crystal structure of endolysin gp46 from Pseudomonas aeruginosa bacteriophage vB_PaeM_KTN6

Components

Glycoside hydrolase family protein

Keywords

HYDROLASE / endolysin / phage lysozyme / muramidase / antimicrobial

Function / homology

: / Glycoside hydrolase, family 19, catalytic / Chitinase class I / chitinase activity / chitin catabolic process / cell wall macromolecule catabolic process / Lysozyme-like domain superfamily / DI(HYDROXYETHYL)ETHER / Glycoside hydrolase family protein

Function and homology information

Biological species

Bacteriophage sp. (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.391 Å

Authors

van Raaij, M.J. / Sanz-Gaitero, M.

Funding support

Spain, 2items

Citation

Journal: Phage (New Rochelle) / Year: 2024
Title: Structural and Biochemical Characterization of a New Phage-Encoded Muramidase, KTN6 Gp46.
Authors: Sanz-Gaitero, M. / De Maesschalck, V. / Patel, A. / Longin, H. / Van Noort, V. / Rodriguez-Rubio, L. / van Ryne, M. / Danis-Wlodarczyk, K. / Drulis-Kawa, Z. / Mesnage, S. / van Raaij, M. / Lavigne, R.

History

Deposition	Jun 1, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 8, 2024	Provider: repository / Type: Initial release
Revision 1.1	Aug 21, 2024	Group: Database references / Category: citation Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8p8e.cif.gz	105.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8p8e.ent.gz		Display	PDB format
PDBx/mmJSON format	8p8e.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8p8e_validation.pdf.gz	428.8 KB	Display	wwPDB validaton report
Full document	8p8e_full_validation.pdf.gz	429.1 KB	Display
Data in XML	8p8e_validation.xml.gz	12.9 KB	Display
Data in CIF	8p8e_validation.cif.gz	18.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p8/8p8e ftp://data.pdbj.org/pub/pdb/validation_reports/p8/8p8e	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

AAA: Glycoside hydrolase family protein

hetero molecules

24.8 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)	41.796, 43.201, 126.181
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Glycoside hydrolase family protein Mass: 24199.422 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteriophage sp. (virus) / Gene: IDBGMNHM_00003 / Plasmid: pEXP5-CT/TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): Lemo21 / Variant (production host): DE3 / References: UniProt: A0A9E7MJ36
#2: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.37 Å³/Da / Density % sol: 48.05 % / Description: needle
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 10 mM HEPES-NaOH pH 7.0; 10 mM trisodium citrate; 16% (w/v) PEG 6000

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97929 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 27, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97929 Å / Relative weight: 1
Reflection	Resolution: 1.39→43.2 Å / Num. obs: 46757 / % possible obs: 99.9 % / Redundancy: 6.4 % / B_iso Wilson estimate: 17.995 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.059 / R_pim(I) all: 0.026 / Net I/σ(I): 15.8
Reflection shell	Resolution: 1.39→1.47 Å / Redundancy: 6.4 % / R_merge(I) obs: 1.002 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 6679 / CC_1/2: 0.695 / R_pim(I) all: 0.425 / % possible all: 99.7

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS	Nov 1, 2016	data reduction
Aimless	0.5.31	data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.391→40.003 Å / Cor.coef. F_o:F_c: 0.982 / Cor.coef. F_o:F_c free: 0.972 / SU B: 2.033 / SU ML: 0.035 / Cross valid method: FREE R-VALUE / ESU R: 0.048 / ESU R Free: 0.049
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1641	2227	4.771 %
R_work	0.1263	44455	-
all	0.128	-	-
obs	-	46682	99.767 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 27.118 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.292 Å²	0 Å²	0 Å²
2-	-	0.645 Å²	-0 Å²
3-	-	-	-0.353 Å²

Refinement step

Cycle: LAST / Resolution: 1.391→40.003 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1686	0	25	234	1945

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	1761
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	1677
X-RAY DIFFRACTION	r_angle_refined_deg	1.419	1.642	2387
X-RAY DIFFRACTION	r_angle_other_deg	1.457	1.581	3844
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.376	5	223
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.048	21.429	98
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.992	15	288
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.032	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	228
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	2025
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	431
X-RAY DIFFRACTION	r_nbd_refined	0.211	0.2	362
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.17	0.2	1512
X-RAY DIFFRACTION	r_nbtor_refined	0.167	0.2	896
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.077	0.2	820
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.145	0.2	127
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.241	0.2	7
X-RAY DIFFRACTION	r_nbd_other	0.258	0.2	45
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.102	0.2	20
X-RAY DIFFRACTION	r_mcbond_it	2.363	2.485	877
X-RAY DIFFRACTION	r_mcbond_other	2.357	2.48	876
X-RAY DIFFRACTION	r_mcangle_it	2.942	3.739	1096
X-RAY DIFFRACTION	r_mcangle_other	2.941	3.745	1097
X-RAY DIFFRACTION	r_scbond_it	3.673	2.964	884
X-RAY DIFFRACTION	r_scbond_other	3.671	2.964	885
X-RAY DIFFRACTION	r_scangle_it	4.432	4.258	1288
X-RAY DIFFRACTION	r_scangle_other	4.43	4.259	1289
X-RAY DIFFRACTION	r_lrange_it	4.688	31.399	2074
X-RAY DIFFRACTION	r_lrange_other	4.394	30.793	2026
X-RAY DIFFRACTION	r_rigid_bond_restr	1.76	3	3437

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.391-1.427	0.362	147	0.305	3211	0.308	3373	0.848	0.879	99.5553	0.298
1.427-1.466	0.261	164	0.254	3142	0.254	3314	0.904	0.902	99.7586	0.242
1.466-1.509	0.233	145	0.212	3073	0.213	3237	0.933	0.93	99.413	0.196
1.509-1.555	0.184	162	0.149	2957	0.151	3129	0.952	0.959	99.6804	0.129
1.555-1.606	0.195	124	0.134	2947	0.136	3073	0.947	0.962	99.9349	0.112
1.606-1.662	0.157	116	0.111	2856	0.112	2973	0.97	0.974	99.9664	0.093
1.662-1.725	0.161	129	0.11	2704	0.112	2833	0.966	0.975	100	0.093
1.725-1.795	0.17	119	0.105	2615	0.107	2735	0.967	0.976	99.9634	0.088
1.795-1.875	0.154	139	0.099	2508	0.102	2647	0.97	0.98	100	0.085
1.875-1.966	0.161	110	0.1	2418	0.103	2530	0.972	0.979	99.9209	0.088
1.966-2.072	0.135	103	0.096	2313	0.098	2416	0.979	0.986	100	0.088
2.072-2.198	0.148	109	0.098	2169	0.1	2278	0.975	0.984	100	0.092
2.198-2.349	0.168	100	0.102	2068	0.105	2169	0.968	0.981	99.9539	0.1
2.349-2.537	0.148	129	0.104	1892	0.107	2022	0.974	0.982	99.9505	0.105
2.537-2.778	0.135	100	0.102	1764	0.104	1867	0.982	0.984	99.8393	0.108
2.778-3.103	0.177	102	0.121	1591	0.125	1699	0.963	0.977	99.6469	0.131
3.103-3.58	0.133	92	0.121	1419	0.122	1516	0.977	0.98	99.6702	0.139
3.58-4.376	0.16	59	0.12	1234	0.121	1296	0.976	0.983	99.7685	0.145
4.376-6.152	0.173	56	0.164	973	0.165	1038	0.975	0.975	99.1329	0.204
6.152-40.003	0.219	22	0.184	601	0.185	629	0.951	0.971	99.0461	0.251

-
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