PDB-4dq5: Structural Investigation of Bacteriophage Phi6 Lysin (WT)

ID or keywords:

Entry

Database: PDB / ID: 4dq5

Title

Structural Investigation of Bacteriophage Phi6 Lysin (WT)

Components

Membrane protein Phi6 P5wt

Keywords

MEMBRANE PROTEIN / lysin / transglycosylase / thermotolerance

Function / homology

Peptidase U40 / Peptidase U40 / Peptidoglycan hydrolase Gp5 superfamily / Peptidase U40 / Lysozyme / Orthogonal Bundle / Mainly Alpha / 4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE / Membrane protein

Function and homology information

Biological species

Pseudomonas phage phi6 (bacteriophage)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.395 Å

Authors

Dessau, M.A. / Modis, Y.

Citation

Journal: PLoS Genet / Year: 2012
Title: Selective pressure causes an RNA virus to trade reproductive fitness for increased structural and thermal stability of a viral enzyme.
Authors: Dessau, M. / Goldhill, D. / McBride, R. / McBride, R.L. / Turner, P.E. / Modis, Y.

History

Deposition	Feb 15, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 2, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jan 23, 2013	Group: Data collection
Revision 1.2	Feb 1, 2017	Group: Database references
Revision 1.3	Nov 15, 2017	Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4	Feb 28, 2024	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4dq5.cif.gz	157.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4dq5.ent.gz	125.8 KB	Display	PDB format
PDBx/mmJSON format	4dq5.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4dq5_validation.pdf.gz	448.6 KB	Display	wwPDB validaton report
Full document	4dq5_full_validation.pdf.gz	450.2 KB	Display
Data in XML	4dq5_validation.xml.gz	19.9 KB	Display
Data in CIF	4dq5_validation.cif.gz	30 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dq/4dq5 ftp://data.pdbj.org/pub/pdb/validation_reports/dq/4dq5	HTTPS FTP

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Related structure data

Related structure data	4dq7C 4dqjC C: citing same article (ref.)
Similar structure data	3on9-2 5guy-2 6npa-4 4a1v-1 2gwo-2 1ckk-d 6kpq-d 4dq7-2 2374 2l7l-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 - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Membrane protein Phi6 P5wt

B: Membrane protein Phi6 P5wt

hetero molecules

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

1

A: Membrane protein Phi6 P5wt

hetero molecules

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

2

B: Membrane protein Phi6 P5wt

hetero molecules

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

Unit cell

Length a, b, c (Å)	62.159, 68.785, 90.045
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Membrane protein Phi6 P5wt / P5a Mass: 19042.375 Da / Num. of mol.: 2 / Fragment: UNP residues 48-220 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas phage phi6 (bacteriophage) / Gene: P5, p5a / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q283U5
#2: Chemical	ChemComp-AES / 4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE / AEBSF Mass: 203.234 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₀FNO₂S / Comment: protease inhibitor*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 479 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.53 Å³/Da / Density % sol: 51.33 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.6 M Na-Acetate, 0.1 M Na-Citrate, pH 6.5, vapor diffusion, hanging drop, temperature 289K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X29A / Wavelength: 1.075 Å

Detector

Date: Jan 1, 2011

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.075 Å / Relative weight: 1

Reflection

Resolution: 1.395→60 Å / Num. obs: 77074 / % possible obs: 99.8 % / Redundancy: 4.9 % / R_merge(I) obs: 0.058 / Χ²: 1.102 / Net I/σ(I): 10.6

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.395-1.42	4.1	0.638	3829	0.408	1	100
1.42-1.45	4.1	0.543	3805	0.419	1	100
1.45-1.48	4.1	0.413	3807	0.439	1	99.9
1.48-1.51	4.1	0.332	3796	0.445	1	100
1.51-1.54	4.1	0.288	3823	0.481	1	100
1.54-1.58	4.1	0.244	3814	0.492	1	100
1.58-1.62	4.1	0.198	3825	0.514	1	100
1.62-1.66	4.2	0.155	3832	0.538	1	99.9
1.66-1.71	4.1	0.131	3800	0.564	1	100
1.71-1.76	4.2	0.112	3829	0.61	1	99.9
1.76-1.83	4.2	0.092	3857	0.663	1	99.9
1.83-1.9	4.2	0.079	3817	0.783	1	99.9
1.9-1.99	4.4	0.084	3840	0.948	1	99.7
1.99-2.09	4.8	0.098	3860	1.219	1	100
2.09-2.22	5.3	0.103	3877	1.634	1	100
2.22-2.39	6.2	0.096	3867	1.832	1	100
2.39-2.63	7.7	0.084	3880	1.736	1	100
2.63-3.02	8.1	0.063	3920	1.78	1	100
3.02-3.8	7.1	0.045	3941	1.927	1	99.9
3.8-60	4.1	0.033	4055	1.373	1	97.6

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
PHENIX	1.7.3_928	refinement
PDB_EXTRACT	3.1	data extraction
HKL-2000		data collection
HKL-2000		data reduction
HKL2Map		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.395→37.67 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.19 / σ(F): 1.36 / Phase error: 16.01 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1773	7698	10 %
R_work	0.1645	-	-
obs	0.1657	77006	99.47 %
all	-	77074	-

Solvent computation

Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 42.142 Å² / k_sol: 0.347 e/Å³

Displacement parameters

B_iso max: 79 Å² / B_iso mean: 25.4023 Å² / B_iso min: 10.08 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.657 Å²	0 Å²	-0 Å²
2-	-	1.1565 Å²	-0 Å²
3-	-	-	-1.8135 Å²

Refinement step

Cycle: LAST / Resolution: 1.395→37.67 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2541	0	26	479	3046

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	2698
X-RAY DIFFRACTION	f_angle_d	1.017	3668
X-RAY DIFFRACTION	f_chiral_restr	0.056	385
X-RAY DIFFRACTION	f_plane_restr	0.005	482
X-RAY DIFFRACTION	f_dihedral_angle_d	14.406	992

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.395-1.4113	0.3285	226	0.3158	2049	2275	89
1.4113-1.4279	0.3231	254	0.3024	2280	2534	100
1.4279-1.4453	0.2844	255	0.2745	2306	2561	100
1.4453-1.4636	0.2708	254	0.2464	2275	2529	100
1.4636-1.4828	0.2608	256	0.2297	2306	2562	100
1.4828-1.5031	0.2381	256	0.2167	2302	2558	100
1.5031-1.5246	0.2306	255	0.2082	2299	2554	100
1.5246-1.5474	0.2113	254	0.1911	2280	2534	100
1.5474-1.5715	0.2154	255	0.1822	2297	2552	100
1.5715-1.5973	0.2007	258	0.177	2323	2581	100
1.5973-1.6249	0.1907	253	0.1685	2268	2521	100
1.6249-1.6544	0.1827	255	0.1569	2298	2553	100
1.6544-1.6862	0.1924	258	0.1606	2323	2581	100
1.6862-1.7206	0.1761	257	0.1549	2310	2567	100
1.7206-1.7581	0.1791	253	0.1565	2279	2532	100
1.7581-1.799	0.1724	258	0.1595	2322	2580	100
1.799-1.8439	0.1738	255	0.1588	2294	2549	100
1.8439-1.8938	0.183	259	0.1607	2334	2593	100
1.8938-1.9495	0.1821	256	0.1569	2300	2556	100
1.9495-2.0124	0.1678	255	0.1561	2298	2553	100
2.0124-2.0844	0.1718	260	0.1591	2336	2596	100
2.0844-2.1678	0.1791	256	0.1556	2306	2562	100
2.1678-2.2665	0.153	260	0.1483	2344	2604	100
2.2665-2.3859	0.1575	259	0.1414	2333	2592	100
2.3859-2.5354	0.166	258	0.1479	2326	2584	100
2.5354-2.7311	0.1729	263	0.158	2361	2624	100
2.7311-3.0058	0.1872	262	0.1672	2354	2616	100
3.0058-3.4405	0.1714	263	0.1636	2375	2638	100
3.4405-4.3337	0.1474	264	0.1489	2385	2649	100
4.3337-37.67	0.1832	271	0.1754	2445	2716	97

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	1.6674	0.1509	-0.1313	1.0727	-0.5776	0.8466	0.0587	0.0716	-0.247	-0.1294	-0.224	-0.0888	0.2549	0.1439	-0.0083	0.2254	0.0333	0.0627	0.1735	0.0281	0.203	20.0066	33.4708	-2.2247
2	0.6768	0.0001	0.0188	0.8885	-0.1718	0.9605	-0.0135	-0.0203	-0.0354	0.0181	-0.1142	-0.1448	0.1001	0.1446	0.0001	0.1672	0.0316	0.0398	0.162	0.0463	0.1789	18.9038	38.2577	3.2341
3	2.8859	-0.2505	0.6041	1.7421	-0.1584	0.8359	-0.0137	-0.1843	-0.5889	0.3674	0.182	0.3854	0.2211	-0.4641	0.0706	0.1943	-0.0107	0.0671	0.2199	0.0672	0.2916	4.2106	31.8164	9.147
4	0.9246	-0.2766	-0.2052	1.6567	-0.1767	0.9871	-0.0673	0.0288	-0.1513	0.0127	0.0406	0.117	0.1324	-0.1437	-0.0301	0.154	-0.0123	0.0294	0.1426	0.0216	0.1631	6.8606	37.0407	2.8005
5	0.9981	0.0345	-0.3807	0.5856	-0.0504	0.8085	0.029	-0.0273	0.2727	0.0608	0.1085	0.0329	-0.0968	-0.0944	0.008	0.1504	0.0338	0.0391	0.1601	0.0308	0.1888	5.6656	51.7453	4.0227
6	4.911	-0.5823	-1.0686	1.5118	-1.6046	2.3699	-0.1761	-0.5884	0.3488	0.2687	0.0473	-0.2572	-0.2397	0.6127	0.0213	0.2389	0.0022	-0.0127	0.404	-0.0887	0.2043	14.052	52.4388	14.3613
7	0.5098	-0.1959	-0.408	1.1209	-0.2628	2.2228	0.2512	0.1071	0.4822	0.129	-0.0979	-0.031	-0.3754	0.3511	0.1659	0.1968	-0.0014	0.0684	0.1978	0.0434	0.2782	11.8358	58.0197	-0.3995
8	1.9041	-0.6974	-0.6047	2.1797	-0.3504	1.9418	-0.1068	-0.1416	0.046	-0.1286	0.1835	0.2557	-0.2057	-0.3019	0.043	0.1402	0.002	0.0342	0.2441	0.0291	0.1825	-23.0251	47.7542	22.8269
9	1.0163	-0.1283	0.2538	1.3803	0.1945	0.6079	-0.0665	-0.4068	0.0783	0.1074	0.0568	0.0189	-0.144	-0.1637	0.0054	0.2123	0.047	0.0354	0.1718	-0.0171	0.1434	-15.277	48.7494	27.6349
10	1.0798	-0.4029	0.6615	1.0348	-0.5991	1.8589	-0.0385	0.1122	0.0174	0.0091	0.0183	-0.0479	0.1	0.1545	0.0022	0.13	0.021	0.005	0.1346	0.0025	0.1252	-7.3558	43.2218	17.7573
11	1.3072	-0.6905	0.3818	1.796	-0.6463	1.104	-0.0708	-0.0883	0.1696	0.4305	-0.0016	-0.2874	-0.0808	0.0992	0.0104	0.1738	0.0448	-0.0558	0.1729	-0.0363	0.1785	2.8129	42.407	30.7698

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 48:81)	A	48 - 81
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 82:118)	A	82 - 118
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 119:134)	A	119 - 134
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 135:163)	A	135 - 163
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 164:191)	A	164 - 191
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 192:200)	A	192 - 200
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 201:220)	A	201 - 220
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 61:81)	B	61 - 81
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 82:106)	B	82 - 106
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 107:191)	B	107 - 191
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 192:220)	B	192 - 220

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