PDB-4exm: The crystal structure of an engineered phage lysin containing the...

ID or keywords:

Entry

Database: PDB / ID: 4exm

Title

The crystal structure of an engineered phage lysin containing the binding domain of pesticin and the killing domain of T4-lysozyme

Components

Pesticin, Lysozyme Chimera

Keywords

TOXIN / HYDROLASE / bacterial lysin

Function / homology

Function and homology information

viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / host cell cytoplasm / defense response to bacterium
Similarity search - Function

Biological species

Yersinia pestis (bacteria)

Enterobacteria phage T4 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Seddiki, N. / Noinaj, N. / Fairman, J.W. / Lukacik, P. / Barnard, T.J. / Buchanan, S.K.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural engineering of a phage lysin that targets Gram-negative pathogens.
Authors: Lukacik, P. / Barnard, T.J. / Keller, P.W. / Chaturvedi, K.S. / Seddiki, N. / Fairman, J.W. / Noinaj, N. / Kirby, T.L. / Henderson, J.P. / Steven, A.C. / Hinnebusch, B.J. / Buchanan, S.K.

History

Deposition	Apr 30, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 20, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jul 4, 2012	Group: Database references
Revision 1.2	Jul 26, 2017	Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3	Sep 13, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4exm.cif.gz	507.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4exm.ent.gz	421.8 KB	Display	PDB format
PDBx/mmJSON format	4exm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4exm_validation.pdf.gz	466.6 KB	Display	wwPDB validaton report
Full document	4exm_full_validation.pdf.gz	486 KB	Display
Data in XML	4exm_validation.xml.gz	43.8 KB	Display
Data in CIF	4exm_validation.cif.gz	59.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ex/4exm ftp://data.pdbj.org/pub/pdb/validation_reports/ex/4exm	HTTPS FTP

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Related structure data

Related structure data	4epaC 4epfSC 4epiC 2lzmS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4epi-1 5w33-2 3vva-d 6mg7-d 6w5l-d 6oej-1 6yjb-1 1oyh-d 1z2l-d 2v8v-2 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 (6) #100 - Apr 2008 Adrenergic Receptors similarity (6) #136 - Apr 2011 Nanobodies similarity (6) #164 - Aug 2013 Serotonin Receptor similarity (6) #217 - Jan 2018 Opioid Receptors similarity (4)

Deposited unit

A: Pesticin, Lysozyme Chimera

B: Pesticin, Lysozyme Chimera

C: Pesticin, Lysozyme Chimera

D: Pesticin, Lysozyme Chimera

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

1

A: Pesticin, Lysozyme Chimera

D: Pesticin, Lysozyme Chimera

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

2

B: Pesticin, Lysozyme Chimera

C: Pesticin, Lysozyme Chimera

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

Unit cell

Length a, b, c (Å)	108.427, 108.427, 109.752
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	145
Space group name H-M	P3₂

#1: Protein	Pesticin, Lysozyme Chimera / Endolysin / Lysis protein / Muramidase Mass: 39700.004 Da / Num. of mol.: 4 / Fragment: SEE REMARK 999 / Mutation: G182R,C267T,C267A,R307I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria), (gene. exp.) Enterobacteria phage T4 (virus) Gene: pst, YP_pPCP06, YPPCP1.05c, E / Production host: Escherichia coli (E. coli) / References: UniProt: Q57159, UniProt: P00720, lysozyme
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	PROTEIN IS A CHIMERA COMPRISING RESIDUES 1-167 OF PESTICIN (UNP Q57159) AND RESIDUES 4-165 OF T4 ...PROTEIN IS A CHIMERA COMPRISING RESIDUES 1-167 OF PESTICIN (UNP Q57159) AND RESIDUES 4-165 OF T4 LYSOZYME (UNP P00720).

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.35 Å³/Da / Density % sol: 47.56 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% w/v PEG3350, 0.25 M calcium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 1, 2011
Radiation	Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.6→30 Å / Num. all: 44328 / Num. obs: 44328 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.9 % / R_sym value: 0.073 / Net I/σ(I): 19.5
Reflection shell	Resolution: 2.6→2.69 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 1.9 / R_sym value: 0.773 / % possible all: 99.7

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Processing

Software

Name	Version	Classification
SERGUI		data collection
PHASER		phasing
PHENIX	(phenix.refine: dev_1038)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 4EPF AND 2LZM

4epf

2lzm

Resolution: 2.6→29.801 Å / SU ML: 0.42 / σ(F): 2.01 / Phase error: 30.41 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2513	2238	5.05 %	RANDOM
R_work	0.1986	-	-	-
obs	0.2014	44328	99.89 %	-
all	-	44328	-	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.6→29.801 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9800	0	0	75	9875

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	9952
X-RAY DIFFRACTION	f_angle_d	0.967	13440
X-RAY DIFFRACTION	f_dihedral_angle_d	15.83	3717
X-RAY DIFFRACTION	f_chiral_restr	0.066	1531
X-RAY DIFFRACTION	f_plane_restr	0.003	1738

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 (%)
2.6-2.6566	0.3821	158	0.3067	2645	X-RAY DIFFRACTION	100
2.6566-2.7183	0.3845	153	0.2998	2627	X-RAY DIFFRACTION	100
2.7183-2.7863	0.3478	137	0.2738	2605	X-RAY DIFFRACTION	100
2.7863-2.8616	0.3585	120	0.2522	2646	X-RAY DIFFRACTION	100
2.8616-2.9457	0.3036	136	0.2545	2614	X-RAY DIFFRACTION	100
2.9457-3.0407	0.3325	134	0.2435	2651	X-RAY DIFFRACTION	100
3.0407-3.1492	0.3536	148	0.2332	2639	X-RAY DIFFRACTION	100
3.1492-3.2752	0.2972	127	0.2323	2640	X-RAY DIFFRACTION	100
3.2752-3.424	0.2626	144	0.2202	2619	X-RAY DIFFRACTION	100
3.424-3.6043	0.2878	139	0.2111	2636	X-RAY DIFFRACTION	100
3.6043-3.8297	0.2594	148	0.2003	2614	X-RAY DIFFRACTION	100
3.8297-4.1246	0.2672	144	0.1914	2618	X-RAY DIFFRACTION	100
4.1246-4.5384	0.232	130	0.1661	2661	X-RAY DIFFRACTION	100
4.5384-5.1921	0.2008	149	0.1589	2630	X-RAY DIFFRACTION	100
5.1921-6.5302	0.2437	130	0.1984	2626	X-RAY DIFFRACTION	100
6.5302-29.8034	0.1864	141	0.1722	2619	X-RAY DIFFRACTION	99

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	5.8149	-2.2379	1.5053	5.2673	-0.841	5.0091	-0.1033	-0.4687	0.0523	0.4	0.1131	-0.0576	-0.0358	-0.2825	-0.0427	0.4774	-0.0186	0.0109	0.3963	-0.0478	0.2803	10.5417	30.4317	1.1835
2	4.5204	-0.621	2.4337	6.18	1.6024	4.1475	-0.1476	-1.7943	0.0315	-0.2389	0.4889	-0.6874	0.2806	1.8004	-0.4167	0.7977	0.3262	0.1484	1.4821	-0.0535	0.8072	39.9263	12.2081	2.0745
3	8.0296	-0.5002	-1.7602	7.9049	1.8089	8.5896	-0.2652	0.7316	-0.0274	-0.9578	0.1424	0.9494	0.1918	-0.5853	0.1799	0.6325	-0.0178	0.0345	0.5879	0.0995	0.7415	34.9665	11.7446	-13.7724
4	6.4042	2.2009	-0.8567	5.9425	-1.2485	5.9656	0.0724	0.088	-0.4198	-0.0429	-0.1149	0.2506	0.0503	-0.6152	-0.1062	0.5296	-0.0231	0.017	0.513	-0.0375	0.3508	3.2576	27.4347	-25.4108
5	6.381	2.0289	-0.5911	5.7484	-0.9355	6.0239	-0.0814	0.5732	-0.0522	-0.5399	0.2271	-0.025	0.118	-0.2543	-0.0573	0.4967	0.0203	0.0169	0.3522	-0.0425	0.299	13.4979	34.1509	-35.2792
6	7.3598	1.1168	1.9702	5.3643	1.5534	7.1016	-0.5446	1.9939	0.32	-0.409	0.7404	-0.3285	-0.6258	1.5833	-0.0991	0.7115	-0.3819	-0.0717	1.1231	0.0972	0.797	37.8087	52.334	-32.7767
7	8.7211	0.0447	3.2233	4.5365	1.9089	6.9592	0.1509	2.03	-0.905	-0.1134	0.3676	-0.6695	0.46	1.8322	-0.5658	0.5382	-0.0729	-0.1054	1.0385	-0.1175	0.9437	38.3463	43.5459	-32.2035
8	9.5503	-0.3209	3.3296	4.6194	2.0088	6.9608	-0.367	-1.3779	0.0234	1.1839	0.4522	0.4137	0.135	-0.446	-0.0699	0.841	0.0694	0.0191	0.6657	0.0995	0.6773	36.0628	50.6266	-12.5228
9	2.0053	-0.2603	1.3814	4.7454	0.6285	6.8135	-1.0201	0.1304	1.5296	0.1533	0.3297	0.9368	-1.1529	-0.192	0.5865	0.7496	0.0716	-0.1586	0.4874	0.0074	1.0409	32.4142	59.5849	-19.8233
10	3.8746	3.0056	0.7009	6.644	2.0363	0.6162	-0.1883	0.0134	-0.5127	-1.0312	0.2159	-0.1675	-0.4319	-0.5898	-0.0798	0.8092	-0.048	0.0325	0.6631	-0.0113	0.5057	5.0775	15.6017	-29.4116
11	5.2561	-0.3752	-0.3757	6.6348	-0.1015	8.7889	0.1714	-0.3602	-0.4232	0.2098	-0.1294	-0.0205	0.3899	0.0265	-0.0932	0.4982	-0.1094	-0.0766	0.4355	-0.0084	0.4579	-3.2306	2.5456	-24.7374
12	1.978	0.6469	0.1158	2.1596	3.3688	7.8637	-0.0352	0.3648	0.1451	-0.6136	0.325	-0.4502	-0.9919	-0.42	-0.3244	0.8264	-0.0736	-0.0129	0.5701	0.0623	0.6503	4.8693	-28.5251	-30.1052
13	3.215	-2.9481	-0.6615	6.4513	2.1428	0.9966	-0.354	-0.0012	0.5897	0.7852	0.3396	-0.1625	0.4609	-0.5488	-0.035	0.8048	0.0842	-0.0387	0.7095	-0.0198	0.5242	5.2173	47.0608	-1.9903
14	4.9435	1.0554	0.8369	6.2848	0.1634	8.0721	0.1559	0.4187	0.4013	-0.2383	-0.0548	0.016	-0.4672	-0.005	-0.1344	0.5125	0.1165	0.0658	0.4463	-0.0068	0.4664	-3.2956	60.0096	-6.4669
15	1.5956	-0.6135	-0.1429	2.0341	3.5226	5.9686	-0.0876	-0.3846	-0.078	0.6054	0.3404	-0.4507	0.9093	-0.575	-0.2136	0.9219	0.0909	0.0287	0.6447	0.0928	0.6997	4.7827	91.1213	-1.2946

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 19 through 169 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 170 through 229 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 230 through 333 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 19 through 63 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 64 through 169 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 170 through 191 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 192 through 249 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 250 through 312 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 313 through 332 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 3 through 45 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 46 through 157 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 158 through 333 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 3 through 45 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 46 through 157 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 158 through 333 )

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