PDB-4dq7: Structural Investigation of Bacteriophage Phi6 Lysin (V207F mutant)

ID or keywords:

Entry

Database: PDB / ID: 4dq7

Title

Structural Investigation of Bacteriophage Phi6 Lysin (V207F mutant)

Components

Membrane protein Phi6 P5

Keywords

HYDROLASE / lysin / transglycosylase / thermotolerance

Function / homology

Peptidase U40 / Peptidase U40 / Peptidoglycan hydrolase Gp5 superfamily / Peptidase U40 / Lysozyme / Orthogonal Bundle / Mainly Alpha / Membrane protein

Function and homology information

Biological species

Pseudomonas phage phi6 (bacteriophage)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.4 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	Feb 1, 2017	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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	4dq7.cif.gz	205 KB	Display	PDBx/mmCIF format
PDB format	pdb4dq7.ent.gz	168.5 KB	Display	PDB format
PDBx/mmJSON format	4dq7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4dq7_validation.pdf.gz	432.7 KB	Display	wwPDB validaton report
Full document	4dq7_full_validation.pdf.gz	434.6 KB	Display
Data in XML	4dq7_validation.xml.gz	18.2 KB	Display
Data in CIF	4dq7_validation.cif.gz	26.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dq/4dq7 ftp://data.pdbj.org/pub/pdb/validation_reports/dq/4dq7	HTTPS FTP

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Related structure data

Related structure data	4dq5C 4dqjC C: citing same article (ref.)
Similar structure data	3w30-1 5lfz-d 3iuy-2 4kak-1 6t5l-2 5hpi-1 3t36-3 5a0x-2 4k60-d 4hjy-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 - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Membrane protein Phi6 P5

B: Membrane protein Phi6 P5

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

1

A: Membrane protein Phi6 P5

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

2

B: Membrane protein Phi6 P5

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

Unit cell

Length a, b, c (Å)	62.120, 68.722, 89.893
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Membrane protein Phi6 P5 / P5a Mass: 19090.418 Da / Num. of mol.: 2 / Fragment: UNP residues 48-220 / Mutation: V207F 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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Membrane protein Phi6 P5 / P5a

Mass: 19090.418 Da / Num. of mol.: 2 / Fragment: UNP residues 48-220 / Mutation: V207F
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: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.51 Å³/Da / Density % sol: 51.05 %
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: 1.4→50 Å / Num. all: 77799 / Num. obs: 73877 / % possible obs: 96.5 % / Redundancy: 4.3 % / R_merge(I) obs: 0.052 / Net I/σ(I): 12.4

Reflection shell

Resolution (Å)	Redundancy (%)	Diffraction-ID	% possible all	R_merge(I) obs
1.4-1.42	4.1	1	94.5
1.42-1.45	4.1	1	94.3
1.45-1.48	4.1	1	94.5
1.48-1.51	4	1	95.3	0.836
1.51-1.54	4	1	95.4	0.663
1.54-1.58	4	1	95.5	0.547
1.58-1.62	4	1	95.8	0.423
1.62-1.66	4	1	96.2	0.312
1.66-1.71	4.1	1	96.3	0.247
1.71-1.76	4.1	1	96.7	0.199
1.76-1.83	4.1	1	96.8	0.156
1.83-1.9	4.1	1	97.4	0.118
1.9-1.99	4.1	1	97.4	0.088
1.99-2.09	4.1	1	97.8	0.07
2.09-2.22	4	1	97.8	0.061
2.22-2.39	4	1	98.3	0.055
2.39-2.63	3.9	1	98.7	0.045
2.63-3.02	5.9	1	98.8	0.073
3.02-3.8	7.5	1	98	0.055
3.8-50	4.4	1	94.7	0.025

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
PHENIX	1.7.3_928	refinement
PDB_EXTRACT	3.1	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.4→41.01 Å / Occupancy max: 1 / Occupancy min: 0.32 / SU ML: 0.2 / σ(F): 1.34 / Phase error: 18.5 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.198	7379	10 %
R_work	0.175	-	-
obs	0.178	73824	96.3 %

Solvent computation

Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 49.01 Å² / k_sol: 0.39 e/Å³

Displacement parameters

B_iso mean: 31.13 Å²

	B_aniso -1	B_aniso -2
1-	0 Å²	0 Å²
2-	-	0 Å²
3-	-	-

Refinement step

Cycle: LAST / Resolution: 1.4→41.01 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2577	0	0	339	2916

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	2726
X-RAY DIFFRACTION	f_angle_d	1.001	3710
X-RAY DIFFRACTION	f_dihedral_angle_d	14.639	996
X-RAY DIFFRACTION	f_chiral_restr	0.131	390
X-RAY DIFFRACTION	f_plane_restr	0.004	488

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 (%)
1.4-1.4143	0.3757	218	0.3712	1986	X-RAY DIFFRACTION	87
1.4143-1.431	0.3865	234	0.3599	2145	X-RAY DIFFRACTION	94
1.431-1.4484	0.3097	242	0.3285	2160	X-RAY DIFFRACTION	94
1.4484-1.4668	0.3412	239	0.2976	2136	X-RAY DIFFRACTION	95
1.4668-1.4861	0.2794	241	0.2743	2143	X-RAY DIFFRACTION	95
1.4861-1.5064	0.2315	242	0.2555	2147	X-RAY DIFFRACTION	95
1.5064-1.5279	0.2357	241	0.2427	2193	X-RAY DIFFRACTION	95
1.5279-1.5507	0.2737	229	0.2193	2171	X-RAY DIFFRACTION	95
1.5507-1.575	0.1871	249	0.2185	2167	X-RAY DIFFRACTION	96
1.575-1.6008	0.243	247	0.2081	2185	X-RAY DIFFRACTION	96
1.6008-1.6284	0.2333	237	0.1895	2191	X-RAY DIFFRACTION	96
1.6284-1.658	0.1925	247	0.1796	2191	X-RAY DIFFRACTION	96
1.658-1.6899	0.1903	243	0.176	2192	X-RAY DIFFRACTION	96
1.6899-1.7244	0.1963	245	0.1769	2199	X-RAY DIFFRACTION	96
1.7244-1.7619	0.2115	247	0.1733	2229	X-RAY DIFFRACTION	97
1.7619-1.8029	0.204	246	0.175	2180	X-RAY DIFFRACTION	97
1.8029-1.848	0.1937	253	0.1734	2257	X-RAY DIFFRACTION	97
1.848-1.8979	0.1808	245	0.1671	2200	X-RAY DIFFRACTION	97
1.8979-1.9538	0.1788	252	0.1665	2252	X-RAY DIFFRACTION	97
1.9538-2.0168	0.181	250	0.1669	2233	X-RAY DIFFRACTION	98
2.0168-2.0889	0.1728	246	0.1606	2246	X-RAY DIFFRACTION	98
2.0889-2.1726	0.1915	247	0.1614	2240	X-RAY DIFFRACTION	98
2.1726-2.2714	0.1711	252	0.1529	2283	X-RAY DIFFRACTION	98
2.2714-2.3912	0.1652	251	0.1484	2266	X-RAY DIFFRACTION	98
2.3912-2.541	0.178	253	0.1569	2286	X-RAY DIFFRACTION	99
2.541-2.7371	0.2032	251	0.1626	2299	X-RAY DIFFRACTION	99
2.7371-3.0125	0.1983	257	0.1787	2297	X-RAY DIFFRACTION	99
3.0125-3.4482	0.1861	258	0.1675	2325	X-RAY DIFFRACTION	98
3.4482-4.3436	0.1675	256	0.1536	2305	X-RAY DIFFRACTION	97
4.3436-41.0262	0.2359	261	0.1936	2341	X-RAY DIFFRACTION	94

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	4.4128	1.9581	0.9061	3.081	-0.3795	0.4618	0.2184	-0.5604	-0.0902	0.1383	-0.5167	-0.1619	0.2342	0.0177	0.2549	0.2886	0.0556	0.101	0.3117	0.1031	0.2765	25.9309	1.7735	4.0535
2	3.7146	-1.3525	-0.0295	4.4711	-1.3585	3.1416	0.0013	0.3438	-0.2003	-0.5335	-0.102	0.1346	0.3856	-0.0964	0.0737	0.2185	0.0184	0.0426	0.1536	-0.0186	0.1479	12.2132	2.5848	-5.9708
3	2.7021	-0.2663	-1.0588	2.5899	-1.6972	4.3647	-0.0431	-0.0949	0.2306	0.1334	-0.2345	-0.5499	-0.0743	0.5466	0.2764	0.2173	0.0109	0.0149	0.2808	0.115	0.3088	23.0298	2.6837	6.5191
4	5.037	0.247	0.237	3.3679	-0.8736	3.0817	-0.1445	-0.5045	-0.484	0.2254	0.2644	0.4381	0.1365	-0.5014	0.0028	0.2231	0.0075	0.0635	0.2876	0.1166	0.3015	6.8061	-0.5901	9.308
5	2.5933	-0.9485	-0.0816	2.6952	-0.9515	2.23	-0.0743	-0.1662	-0.0455	0.0979	0.0876	0.0583	0.033	-0.1706	-0.0066	0.116	-0.0097	0.02	0.1502	0.0034	0.1287	6.7565	9.5187	3.7977
6	8.2822	0.0975	-2.7939	3.8155	-1.5457	6.9315	-0.046	-1.0666	0.4036	0.537	-0.0782	-0.5368	-0.5912	0.8499	0.2001	0.3376	-0.0278	-0.0685	0.5335	-0.0414	0.276	15.6674	17.8831	13.3151
7	3.9724	-0.446	-0.4513	2.9859	-1.4744	5.0808	-0.0329	0.145	0.5903	0.0215	-0.1301	-0.0766	-0.6488	0.1247	0.0348	0.1996	0.0116	0.0164	0.148	0.0182	0.2739	10.6656	24.2626	-0.7956
8	3.4146	-0.7265	-0.33	5.5407	1.058	3.9823	-0.1848	-0.1702	0.0467	0.2146	0.1264	0.5077	-0.1675	-0.3894	0.0581	0.2082	0.0094	0.0273	0.279	-0.0021	0.1752	-22.8189	13.9784	23.017
9	2.0664	-0.6595	-0.0405	3.0219	0.6213	1.8629	-0.1926	-0.4661	0.1557	0.1656	0.184	-0.0676	-0.2509	-0.025	0.0406	0.2693	0.0625	0.0285	0.2156	-0.0266	0.156	-15.2969	14.5101	27.4188
10	5.1024	-0.6765	-0.7693	4.9525	0.1093	6.1894	-0.1985	-0.0216	0.478	0.233	0.0296	-0.3881	-0.5606	0.3709	-0.028	0.2162	-0.0084	-0.0402	0.1901	0.0094	0.2283	-9.447	19.9602	17.3957
11	3.9938	1.2069	-0.2056	7.1166	1.1315	3.9331	-0.0853	0.5564	0.0074	-0.4398	0.2359	-0.3925	0.0077	0.5445	-0.0217	0.1889	0.0137	0.0162	0.2189	0.0203	0.1851	-8.1762	12.3587	8.455
12	2.0266	0.1287	0.0344	4.194	0.5633	2.7654	-0.1513	0.0826	0.0546	0.0665	0.144	0.2274	0.153	-0.2034	-0.03	0.1537	-0.0141	-0.008	0.163	0.0148	0.147	-15.3798	13.9728	9.611
13	6.2141	-2.5736	1.8405	3.5774	-1.3984	2.9614	0.0789	0.2708	-0.3471	-0.1163	-0.0175	0.0705	0.4643	0.0966	-0.039	0.1821	0.0147	0.0213	0.1229	-0.0061	0.1163	-10.5061	4.1188	17.951
14	2.0935	0.0177	0.4767	2.8389	-0.2315	1.7931	-0.1404	0.0452	-0.07	0.2445	0.1651	-0.2966	0.3835	0.4183	-0.0291	0.2445	0.0981	-0.0082	0.2243	-0.0193	0.1907	-0.1396	4.2528	24.7192
15	3.7137	2.0421	-2.2043	5.0265	-1.1178	2.2835	0.2759	-0.0343	0.7448	0.2926	-0.0656	-0.6306	-0.3526	0.6605	-0.2662	0.2978	0.0197	-0.0469	0.3216	-0.0449	0.3951	4.6059	16.0297	26.0974
16	4.4382	-2.0818	0.5099	4.305	-1.024	1.1258	-0.0772	-0.4155	-0.1587	0.5808	0.2219	-0.2102	0.1637	-0.0787	-0.191	0.3352	0.1477	-0.0916	0.2697	-0.0638	0.1734	1.8284	3.512	33.4119

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 48:72)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 73:92)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 93:112)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 113:132)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 133:192)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 193:202)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 203:220)
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 61:81)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 82:106)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 107:118)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 119:127)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 128:141)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 142:163)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 164:191)
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 192:200)
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 201:220)

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