PDB-7q4t: Structure of the Pseudomonas aeruginosa bacteriophage JG004 endol...

ID or keywords:

Entry

Database: PDB / ID: 7q4t

Title

Structure of the Pseudomonas aeruginosa bacteriophage JG004 endolysin Pae87 bound to a peptidoglycan fragment.

Components

ALA-DGL
Endolysin

Keywords

HYDROLASE / endolysin / phage lysozyme / muramidase / monomodular / antimicrobial.

Function / homology

N-acetylmuramidase / N-acetylmuramidase / Lysozyme-like domain superfamily / DI(HYDROXYETHYL)ETHER / Endolysin

Function and homology information

Biological species

Pseudomonas phage JG004 (virus)

Pseudomonas aeruginosa PAO1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.27 Å

Authors

Seoane-Blanco, M. / van Raaij, M.J.

Funding support

Spain, 1items

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Monomodular Pseudomonas aeruginosa phage JG004 lysozyme (Pae87) contains a bacterial surface-active antimicrobial peptide-like region and a possible substrate-binding subdomain.
Authors: Vazquez, R. / Seoane-Blanco, M. / Rivero-Buceta, V. / Ruiz, S. / van Raaij, M.J. / Garcia, P.

History

Deposition	Nov 2, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 23, 2022	Provider: repository / Type: Initial release
Revision 1.1	Apr 13, 2022	Group: Database references / Category: citation Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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.year
Revision 1.2	Jan 31, 2024	Group: Data collection / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.3	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7q4t.cif.gz	98.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7q4t.ent.gz		Display	PDB format
PDBx/mmJSON format	7q4t.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7q4t_validation.pdf.gz	816.3 KB	Display	wwPDB validaton report
Full document	7q4t_full_validation.pdf.gz	817.2 KB	Display
Data in XML	7q4t_validation.xml.gz	11 KB	Display
Data in CIF	7q4t_validation.cif.gz	15.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q4/7q4t ftp://data.pdbj.org/pub/pdb/validation_reports/q4/7q4t	HTTPS FTP

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Related structure data

Related structure data	7q4sSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6a6i-2 5a68-d 7q4s-2 7q4s-1 2het-4 5csi-d 5qnr-2 5qnu-2 2voo-1 2b3s-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

AAA: Endolysin

LbL: ALA-DGL

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	43.581, 61.173, 69.210
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein / Protein/peptide / Sugars , 3 types, 3 molecules AAALbL

#1: Protein

Endolysin

Mass: 23084.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pseudomonas phage JG004 (virus) / Gene: PJG4_087 / Plasmid: pET28a / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F4YDQ3

#2: Protein/peptide

ALA-DGL

Mass: 218.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural)

Pseudomonas aeruginosa PAO1 (bacteria)

#3: Polysaccharide

2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-alpha-muramic acid

Type: oligosaccharide / Mass: 496.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DGlcpNAcb1-4MurNAc1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2NCC/3=O_3OC^RCO/4=O/3C][a2122h-1b_1-5_2*NCC/3=O]/1-2/a4-b1	WURCS	PDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(3+1)][<C3O1>]{}[(4+1)][b-D-GlcpNAc]{}}	LINUCS	PDB-CARE

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Non-polymers , 3 types, 132 molecules

#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	Y

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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 Å³/Da / Density % sol: 38.7 % / Description: bar-shaped
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.12 M Tris-HCl, 20% (w/v) PEG 5000 MME, 8% (v/v) ethylene glycol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97933 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97933 Å / Relative weight: 1
Reflection	Resolution: 1.27→69.21 Å / Num. obs: 49510 / % possible obs: 99.9 % / Redundancy: 6.4 % / B_iso Wilson estimate: 13.938 Å² / CC_1/2: 1 / R_merge(I) obs: 0.042 / R_pim(I) all: 0.018 / R_rim(I) all: 0.046 / Net I/σ(I): 17.6
Reflection shell	Resolution: 1.27→1.29 Å / Redundancy: 6 % / R_merge(I) obs: 0.753 / Mean I/σ(I) obs: 2 / Num. unique obs: 2412 / CC_1/2: 0.903 / R_pim(I) all: 0.33 / R_rim(I) all: 0.825 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS	Jan 31, 2020	data reduction
Aimless	0.7.7	data scaling
MOLREP	11.7.02	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7Q4S

7q4s

Resolution: 1.27→45.854 Å / Cor.coef. F_o:F_c: 0.981 / Cor.coef. F_o:F_c free: 0.975 / SU B: 1.72 / SU ML: 0.031 / Cross valid method: FREE R-VALUE / ESU R: 0.04 / ESU R Free: 0.04
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1608	2454	4.963 %
R_work	0.1304	46988	-
all	0.132	-	-
obs	-	49442	99.81 %

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: 21.016 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.729 Å²	0 Å²	-0 Å²
2-	-	0.137 Å²	0 Å²
3-	-	-	0.592 Å²

Refinement step

Cycle: LAST / Resolution: 1.27→45.854 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1500	0	99	117	1716

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	1643
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	1595
X-RAY DIFFRACTION	r_angle_refined_deg	1.361	1.667	2179
X-RAY DIFFRACTION	r_angle_other_deg	1.445	1.6	3673
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.636	5	187
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.452	23.012	83
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.083	15	276
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.866	15	7
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	200
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	1788
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	375
X-RAY DIFFRACTION	r_nbd_refined	0.247	0.2	348
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.177	0.2	1394
X-RAY DIFFRACTION	r_nbtor_refined	0.173	0.2	805
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.094	0.2	707
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.115	0.2	89
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.249	0.2	8
X-RAY DIFFRACTION	r_nbd_other	0.207	0.2	48
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.165	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	1.671	1.832	754
X-RAY DIFFRACTION	r_mcbond_other	1.671	1.832	754
X-RAY DIFFRACTION	r_mcangle_it	1.951	2.758	939
X-RAY DIFFRACTION	r_mcangle_other	1.95	2.759	940
X-RAY DIFFRACTION	r_scbond_it	2.576	2.307	889
X-RAY DIFFRACTION	r_scbond_other	2.575	2.311	890
X-RAY DIFFRACTION	r_scangle_it	3.208	3.243	1240
X-RAY DIFFRACTION	r_scangle_other	3.207	3.246	1241
X-RAY DIFFRACTION	r_lrange_it	3.244	22.899	1878
X-RAY DIFFRACTION	r_lrange_other	3.066	22.679	1864
X-RAY DIFFRACTION	r_rigid_bond_restr	1.417	3	3238

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
1.27-1.303	0.246	178	0.243	3425	0.243	3605	0.9	0.876	99.9445	0.21
1.303-1.339	0.256	170	0.214	3351	0.216	3521	0.87	0.894	100	0.183
1.339-1.377	0.227	184	0.194	3220	0.196	3411	0.908	0.917	99.7948	0.159
1.377-1.42	0.207	172	0.175	3181	0.177	3353	0.923	0.936	100	0.14
1.42-1.466	0.181	159	0.152	3062	0.153	3223	0.94	0.95	99.9379	0.12
1.466-1.518	0.186	145	0.126	2967	0.129	3118	0.949	0.963	99.8076	0.098
1.518-1.575	0.152	132	0.111	2901	0.112	3035	0.968	0.974	99.9341	0.086
1.575-1.639	0.155	125	0.108	2786	0.111	2913	0.97	0.972	99.9313	0.087
1.639-1.712	0.15	148	0.101	2646	0.104	2800	0.972	0.978	99.7857	0.081
1.712-1.795	0.136	136	0.093	2540	0.096	2684	0.977	0.981	99.7019	0.078
1.795-1.892	0.135	126	0.093	2428	0.095	2557	0.981	0.984	99.8827	0.081
1.892-2.007	0.151	132	0.096	2279	0.099	2417	0.978	0.984	99.7518	0.086
2.007-2.145	0.125	108	0.097	2166	0.098	2279	0.983	0.986	99.7806	0.09
2.145-2.317	0.125	110	0.098	2023	0.099	2142	0.983	0.987	99.5798	0.093
2.317-2.537	0.159	111	0.106	1867	0.108	1981	0.972	0.984	99.8486	0.102
2.537-2.836	0.154	95	0.125	1680	0.126	1784	0.974	0.978	99.4955	0.126
2.836-3.272	0.153	83	0.131	1522	0.132	1611	0.973	0.977	99.6276	0.137
3.272-4.002	0.152	57	0.134	1305	0.135	1367	0.973	0.977	99.6342	0.147
4.002-5.639	0.171	46	0.154	1027	0.154	1083	0.97	0.977	99.0766	0.18
5.639-45.854	0.207	37	0.223	612	0.222	652	0.968	0.965	99.5399	0.258

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