PDB-8bke: Crystal structure of the Klebsiella phage KP34p57 capsular depoly...

ID or keywords:

Entry

Database: PDB / ID: 8bke

Title

Crystal structure of the Klebsiella phage KP34p57 capsular depolymerase

Components

Uncharacterized protein 57

Keywords

VIRAL PROTEIN / phage / capsulae

Function / homology

symbiont entry into host cell via disruption of host cell glycocalyx / symbiont entry into host cell via disruption of host cell envelope / virus tail / adhesion receptor-mediated virion attachment to host cell / Depolymerase, capsule K63-specific

Function and homology information

Biological species

Klebsiella phage KP34 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2 Å

Authors

Berisio, R. / Squeglia, F.

Funding support

Poland, 1items

Citation

Journal: Mbio / Year: 2023
Title: Klebsiella phage KP34gp57 capsular depolymerase structure and function: from a serendipitous finding to the design of active mini-enzymes against K. pneumoniae.
Authors: Maciejewska, B. / Squeglia, F. / Latka, A. / Privitera, M. / Olejniczak, S. / Switala, P. / Ruggiero, A. / Marasco, D. / Kramarska, E. / Drulis-Kawa, Z. / Berisio, R.

History

Deposition	Nov 9, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 30, 2023	Provider: repository / Type: Initial release
Revision 1.1	Mar 20, 2024	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8bke.cif.gz	188.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8bke.ent.gz		Display	PDB format
PDBx/mmJSON format	8bke.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8bke_validation.pdf.gz	322.8 KB	Display	wwPDB validaton report
Full document	8bke_full_validation.pdf.gz	325.4 KB	Display
Data in XML	8bke_validation.xml.gz	23.9 KB	Display
Data in CIF	8bke_validation.cif.gz	34.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bk/8bke ftp://data.pdbj.org/pub/pdb/validation_reports/bk/8bke	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: Uncharacterized protein 57

BBB: Uncharacterized protein 57

135 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

AAA: Uncharacterized protein 57

defined by author
Evidence: light scattering
67.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

BBB: Uncharacterized protein 57

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

Unit cell

Length a, b, c (Å)	38.340, 140.985, 81.925
Angle α, β, γ (deg.)	90.000, 102.633, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Uncharacterized protein 57 Mass: 67706.641 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella phage KP34 (virus) / Gene: 57 / Production host: Escherichia coli (E. coli) / References: UniProt: D1L302
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 416 / 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: 2.35 Å³/Da / Density % sol: 47.62 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 0.04 M cytric acid, 0.06 M bis-tris propane, 20% PEG 3350

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.987 Å
Detector	Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 14, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.987 Å / Relative weight: 1
Reflection	Resolution: 2→30 Å / Num. obs: 203918 / % possible obs: 87.1 % / Redundancy: 4.1 % / R_merge(I) obs: 0.11 / Net I/σ(I): 14.2
Reflection shell	Resolution: 2.2→2.25 Å / R_merge(I) obs: 0.41 / Num. unique obs: 2652 / % possible all: 91.3

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0257	refinement
HKL-2000	HKL2000_712-Linux	data reduction
HKL-2000	HKL2000_712-Linux	data scaling
SOLVE	2.13	phasing
RESOLVE	2.13	model building

Refinement

Method to determine structure:

SAD / Resolution: 2→15 Å / Cor.coef. F_o:F_c: 0.94 / Cor.coef. F_o:F_c free: 0.942 / SU B: 5.47 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / ESU R: 0.288 / ESU R Free: 0.213
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2473	746	1.663 %
R_work	0.2043	44126	-
all	0.205	-	-
obs	-	48807	78.471 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK

Displacement parameters

B_iso mean: 30.55 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.081 Å²	0 Å²	0.038 Å²
2-	-	-0.066 Å²	0 Å²
3-	-	-	-0.029 Å²

Refinement step

Cycle: LAST / Resolution: 2→15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6480	0	0	419	6899

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	6622
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	5972
X-RAY DIFFRACTION	r_angle_refined_deg	1.529	1.63	9020
X-RAY DIFFRACTION	r_angle_other_deg	1.257	1.57	13776
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.719	5	854
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.13	21.395	344
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.9	15	990
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.091	15	50
X-RAY DIFFRACTION	r_chiral_restr	0.062	0.2	880
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	7630
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1496
X-RAY DIFFRACTION	r_nbd_refined	0.19	0.2	1318
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.194	0.2	5956
X-RAY DIFFRACTION	r_nbtor_refined	0.161	0.2	3227
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.075	0.2	3164
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.215	0.2	474
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.108	0.2	7
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.133	0.2	23
X-RAY DIFFRACTION	r_nbd_other	0.187	0.2	82
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.151	0.2	15
X-RAY DIFFRACTION	r_mcbond_it	2.326	3.192	3422
X-RAY DIFFRACTION	r_mcbond_other	2.324	3.191	3421
X-RAY DIFFRACTION	r_mcangle_it	3.323	4.781	4274
X-RAY DIFFRACTION	r_mcangle_other	3.323	4.782	4275
X-RAY DIFFRACTION	r_scbond_it	2.432	3.387	3200
X-RAY DIFFRACTION	r_scbond_other	2.432	3.388	3201
X-RAY DIFFRACTION	r_scangle_it	3.563	4.997	4746
X-RAY DIFFRACTION	r_scangle_other	3.563	4.998	4747
X-RAY DIFFRACTION	r_lrange_it	5.83	38.648	7451
X-RAY DIFFRACTION	r_lrange_other	5.767	38.464	7369

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
2-2.051	0.324	27	0.251	1326	0.252	4146	0.83	0.884	32.6339	0.216
2.051-2.106	0.234	31	0.251	1703	0.251	4041	0.844	0.844	42.9102	0.226
2.106-2.166	0.359	45	0.309	2198	0.31	3935	0.823	0.848	57.0013	0.275
2.166-2.231	0.255	42	0.237	2723	0.237	3827	0.872	0.862	72.2498	0.21
2.231-2.303	0.271	40	0.198	3116	0.199	3684	0.884	0.905	85.6678	0.172
2.303-2.381	0.352	57	0.208	3266	0.21	3616	0.842	0.91	91.8971	0.176
2.381-2.469	0.235	46	0.21	2914	0.21	3446	0.914	0.909	85.8967	0.172
2.469-2.567	0.278	57	0.209	2921	0.21	3377	0.897	0.921	88.1848	0.173
2.567-2.677	0.265	41	0.229	2522	0.23	3181	0.917	0.921	80.5721	0.182
2.677-2.804	0.295	60	0.213	2625	0.215	3066	0.897	0.918	87.5734	0.173
2.804-2.95	0.336	35	0.241	2330	0.243	2958	0.887	0.913	79.9527	0.189
2.95-3.121	0.288	42	0.205	2318	0.207	2739	0.9	0.923	86.1628	0.169
3.121-3.326	0.25	51	0.193	2483	0.194	2622	0.913	0.94	96.6438	0.172
3.326-3.578	0.283	30	0.217	2392	0.217	2464	0.925	0.947	98.2955	0.202
3.578-3.897	0.224	33	0.203	2167	0.203	2273	0.942	0.941	96.7884	0.189
3.897-4.321	0.204	29	0.173	1910	0.173	2072	0.947	0.942	93.5811	0.156
4.321-4.922	0.141	24	0.162	1663	0.161	1831	0.978	0.955	92.1354	0.158
4.922-5.872	0.172	32	0.176	1470	0.176	1586	0.954	0.948	94.7037	0.171
5.872-7.733	0.235	8	0.184	1239	0.185	1296	0.934	0.945	96.2191	0.177
7.733-15	0.198	16	0.192	840	0.192	859	0.945	0.966	99.6508	0.194

-
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