PDB-3hde: Crystal structure of full-length endolysin R21 from phage 21

ID or keywords:

Entry

Database: PDB / ID: 3hde

Title

Crystal structure of full-length endolysin R21 from phage 21

Components

Lysozyme

Keywords

HYDROLASE / lysozyme-like / Antimicrobial / Bacteriolytic enzyme / Glycosidase / Late protein

Function / homology

Function and homology information

peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to bacterium / host cell plasma membrane / membrane
Similarity search - Function

Biological species

Enterobacteria phage P21 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SIRAS / Resolution: 1.95 Å

Authors

Sun, Q. / Arockiasamy, A. / McKee, E. / Caronna, E. / Sacchettini, J.C.

Citation

Journal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Regulation of a muralytic enzyme by dynamic membrane topology.
Authors: Sun, Q. / Kuty, G.F. / Arockiasamy, A. / Xu, M. / Young, R. / Sacchettini, J.C.

History

Deposition	May 7, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 3, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software
Revision 1.3	Oct 30, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3hde.cif.gz	139.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3hde.ent.gz	109.8 KB	Display	PDB format
PDBx/mmJSON format	3hde.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3hde_validation.pdf.gz	449.5 KB	Display	wwPDB validaton report
Full document	3hde_full_validation.pdf.gz	459.2 KB	Display
Data in XML	3hde_validation.xml.gz	28.3 KB	Display
Data in CIF	3hde_validation.cif.gz	40.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hd/3hde ftp://data.pdbj.org/pub/pdb/validation_reports/hd/3hde	HTTPS FTP

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Related structure data

Related structure data	3hdfC C: citing same article (ref.)
Similar structure data	1d5r-d 3f4a-d 2qrj-d 3dmf-d 5b1z-d 2zwv-d 1tfa-d 2zul-d 5bzx-2 4n9w-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#9 - Sep 2000 Lysozyme similarity (4) #217 - Jan 2018 Opioid Receptors similarity (3) #100 - Apr 2008 Adrenergic Receptors similarity (4) #136 - Apr 2011 Nanobodies similarity (4) #164 - Aug 2013 Serotonin Receptor similarity (4)

Deposited unit

A: Lysozyme

B: Lysozyme

C: Lysozyme

D: Lysozyme

72.2 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Lysozyme

B: Lysozyme

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

2

C: Lysozyme

D: Lysozyme

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

Unit cell

Length a, b, c (Å)	78.249, 94.814, 97.650
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Lysozyme / Lysis protein / Muramidase / Endolysin Mass: 18039.926 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage P21 (virus) / Gene: R / Plasmid: pETR21 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: P27359, lysozyme
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y
Sequence details	ACCORDING TO THE AUTHORS RESIDUES PHE 105 AND VAL 106 ARE CORRECT IN THE PDB FILE.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.51 Å³/Da / Density % sol: 51 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 150mM Sodium acetate, 2M sodium formate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

Diffraction	Mean temperature: 120 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9795 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 29, 2008 Details: Si(111) Double Crystal Monochromator. Adjustable focusing mirrors in K-B geometry
Radiation	Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.95→50 Å / Num. obs: 53709 / % possible obs: 99.8 % / Redundancy: 7.1 % / R_merge(I) obs: 0.062 / Χ²: 1.21 / Net I/σ(I): 45.0787
Reflection shell	Resolution: 1.95→2.02 Å / Redundancy: 5.8 % / R_merge(I) obs: 0.421 / Mean I/σ(I) obs: 4.0351 / Num. unique all: 1937 / Χ²: 0.849 / % possible all: 98.9

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Phasing

Phasing	Method: SIRAS

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHELX		phasing
PHENIX		refinement
PDB_EXTRACT	3.005	data extraction
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling
SHELXD		phasing

Refinement

Method to determine structure:

SIRAS / Resolution: 1.95→43.41 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.771 / Stereochemistry target values: ml

	R_factor	Num. reflection	% reflection
R_free	0.248	1552	3.06 %
R_work	0.212	-	-
obs	-	50721	94.6 %

Solvent computation

B_sol: 61.62 Å² / k_sol: 0.35 e/Å³

Displacement parameters

B_iso max: 80.73 Å² / B_iso mean: 40.995 Å² / B_iso min: 21.71 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-17.673 Å²	0 Å²	0 Å²
2-	-	9.626 Å²	0 Å²
3-	-	-	8.047 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→43.41 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4916	0	0	365	5281

Refine LS restraints

Refine-ID	Type	Dev ideal
X-RAY DIFFRACTION	f_angle_d	0.7
X-RAY DIFFRACTION	f_bond_d	0.005
X-RAY DIFFRACTION	f_chiral_restr	0.053
X-RAY DIFFRACTION	f_dihedral_angle_d	9.977
X-RAY DIFFRACTION	f_plane_restr	0.003
X-RAY DIFFRACTION	f_nbd_refined	4.056

LS refinement shell

Resolution (Å)	R_factor R_work	Num. reflection R_work	Refine-ID	Total num. of bins used	% reflection obs (%)
1.95-1.957	0.266	425	X-RAY DIFFRACTION	98	74
1.957-1.964	0.267	410	X-RAY DIFFRACTION	98	79
1.964-1.97	0.295	389	X-RAY DIFFRACTION	98	74
1.97-1.977	0.263	407	X-RAY DIFFRACTION	98	77
1.977-1.984	0.261	449	X-RAY DIFFRACTION	98	80
1.984-1.992	0.254	435	X-RAY DIFFRACTION	98	81
1.992-1.999	0.259	427	X-RAY DIFFRACTION	98	80
1.999-2.006	0.23	448	X-RAY DIFFRACTION	98	80
2.006-2.014	0.261	446	X-RAY DIFFRACTION	98	83
2.014-2.021	0.259	433	X-RAY DIFFRACTION	98	83
2.021-2.029	0.245	461	X-RAY DIFFRACTION	98	84
2.029-2.037	0.271	433	X-RAY DIFFRACTION	98	80
2.037-2.045	0.233	449	X-RAY DIFFRACTION	98	84
2.045-2.053	0.237	469	X-RAY DIFFRACTION	98	86
2.053-2.061	0.249	483	X-RAY DIFFRACTION	98	89
2.061-2.069	0.228	466	X-RAY DIFFRACTION	98	88
2.069-2.078	0.243	462	X-RAY DIFFRACTION	98	86
2.078-2.086	0.229	459	X-RAY DIFFRACTION	98	87
2.086-2.095	0.231	482	X-RAY DIFFRACTION	98	87
2.095-2.104	0.221	466	X-RAY DIFFRACTION	98	85
2.104-2.113	0.22	458	X-RAY DIFFRACTION	98	88
2.113-2.122	0.238	508	X-RAY DIFFRACTION	98	88
2.122-2.132	0.227	443	X-RAY DIFFRACTION	98	88
2.132-2.141	0.234	476	X-RAY DIFFRACTION	98	89
2.141-2.151	0.237	501	X-RAY DIFFRACTION	98	88
2.151-2.161	0.231	486	X-RAY DIFFRACTION	98	89
2.161-2.171	0.246	470	X-RAY DIFFRACTION	98	89
2.171-2.181	0.241	487	X-RAY DIFFRACTION	98	91
2.181-2.192	0.226	482	X-RAY DIFFRACTION	98	89
2.192-2.203	0.237	478	X-RAY DIFFRACTION	98	88
2.203-2.214	0.235	485	X-RAY DIFFRACTION	98	90
2.214-2.225	0.243	503	X-RAY DIFFRACTION	98	93
2.225-2.236	0.222	499	X-RAY DIFFRACTION	98	90
2.236-2.248	0.215	487	X-RAY DIFFRACTION	98	92
2.248-2.259	0.236	475	X-RAY DIFFRACTION	98	90
2.259-2.272	0.225	501	X-RAY DIFFRACTION	98	89
2.272-2.284	0.24	494	X-RAY DIFFRACTION	98	93
2.284-2.296	0.225	486	X-RAY DIFFRACTION	98	92
2.296-2.309	0.231	530	X-RAY DIFFRACTION	98	92
2.309-2.322	0.216	489	X-RAY DIFFRACTION	98	93
2.322-2.336	0.23	489	X-RAY DIFFRACTION	98	91
2.336-2.35	0.221	484	X-RAY DIFFRACTION	98	92
2.35-2.364	0.213	536	X-RAY DIFFRACTION	98	94
2.364-2.378	0.227	495	X-RAY DIFFRACTION	98	93
2.378-2.393	0.228	506	X-RAY DIFFRACTION	98	95
2.393-2.409	0.231	508	X-RAY DIFFRACTION	98	91
2.409-2.424	0.23	509	X-RAY DIFFRACTION	98	93
2.424-2.44	0.238	520	X-RAY DIFFRACTION	98	93
2.44-2.457	0.24	499	X-RAY DIFFRACTION	98	94
2.457-2.474	0.237	496	X-RAY DIFFRACTION	98	94
2.474-2.491	0.223	509	X-RAY DIFFRACTION	98	94
2.491-2.509	0.225	514	X-RAY DIFFRACTION	98	91
2.509-2.527	0.217	516	X-RAY DIFFRACTION	98	96
2.527-2.546	0.234	505	X-RAY DIFFRACTION	98	95
2.546-2.566	0.219	542	X-RAY DIFFRACTION	98	95
2.566-2.586	0.219	484	X-RAY DIFFRACTION	98	95
2.586-2.607	0.23	530	X-RAY DIFFRACTION	98	95
2.607-2.629	0.237	518	X-RAY DIFFRACTION	98	95
2.629-2.651	0.233	509	X-RAY DIFFRACTION	98	95
2.651-2.674	0.236	529	X-RAY DIFFRACTION	98	95
2.674-2.698	0.23	532	X-RAY DIFFRACTION	98	97
2.698-2.723	0.214	527	X-RAY DIFFRACTION	98	96
2.723-2.748	0.24	503	X-RAY DIFFRACTION	98	95
2.748-2.775	0.228	526	X-RAY DIFFRACTION	98	95
2.775-2.803	0.236	540	X-RAY DIFFRACTION	98	95
2.803-2.832	0.226	489	X-RAY DIFFRACTION	98	96
2.832-2.862	0.231	531	X-RAY DIFFRACTION	98	96
2.862-2.893	0.234	540	X-RAY DIFFRACTION	98	96
2.893-2.926	0.221	517	X-RAY DIFFRACTION	98	96
2.926-2.961	0.212	537	X-RAY DIFFRACTION	98	96
2.961-2.997	0.211	512	X-RAY DIFFRACTION	98	96
2.997-3.034	0.226	526	X-RAY DIFFRACTION	98	97
3.034-3.074	0.229	540	X-RAY DIFFRACTION	98	96
3.074-3.116	0.217	521	X-RAY DIFFRACTION	98	97
3.116-3.161	0.235	539	X-RAY DIFFRACTION	98	96
3.161-3.208	0.225	518	X-RAY DIFFRACTION	98	97
3.208-3.258	0.214	548	X-RAY DIFFRACTION	98	97
3.258-3.312	0.221	522	X-RAY DIFFRACTION	98	97
3.312-3.369	0.208	517	X-RAY DIFFRACTION	98	95
3.369-3.43	0.21	543	X-RAY DIFFRACTION	98	97
3.43-3.496	0.221	545	X-RAY DIFFRACTION	98	96
3.496-3.567	0.205	529	X-RAY DIFFRACTION	98	96
3.567-3.645	0.182	533	X-RAY DIFFRACTION	98	97
3.645-3.73	0.187	546	X-RAY DIFFRACTION	98	97
3.73-3.823	0.172	523	X-RAY DIFFRACTION	98	96
3.823-3.926	0.183	544	X-RAY DIFFRACTION	98	96
3.926-4.042	0.186	530	X-RAY DIFFRACTION	98	97
4.042-4.172	0.173	538	X-RAY DIFFRACTION	98	97
4.172-4.321	0.184	546	X-RAY DIFFRACTION	98	97
4.321-4.494	0.2	541	X-RAY DIFFRACTION	98	97
4.494-4.698	0.169	541	X-RAY DIFFRACTION	98	97
4.698-4.945	0.191	549	X-RAY DIFFRACTION	98	97
4.945-5.255	0.182	548	X-RAY DIFFRACTION	98	97
5.255-5.66	0.204	551	X-RAY DIFFRACTION	98	97
5.66-6.228	0.205	549	X-RAY DIFFRACTION	98	97
6.228-7.125	0.205	565	X-RAY DIFFRACTION	98	97
7.125-8.964	0.178	566	X-RAY DIFFRACTION	98	97
8.964-43.418	0.188	562	X-RAY DIFFRACTION	98	89

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