PDB-6e0v: Apo crystal structure of the colanidase tailspike protein gp150 o...

ID or keywords:

Entry

Database: PDB / ID: 6e0v

Title

Apo crystal structure of the colanidase tailspike protein gp150 of Phage Phi92

Components

Bacteriophage Phi92 gp150

Keywords

HYDROLASE / Colanidase / tailspike protein / bacteriophage phi92

Function / homology

Parallel beta-helix repeat / Parallel beta-helix repeats / Pectin lyase fold / Pectin lyase fold/virulence factor / STRONTIUM ION / Phi92_gp150

Function and homology information

Biological species

Enterobacteria phage phi92 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.75 Å

Authors

Leiman, P.G. / Browning, C. / Gerardy-Schahn, R. / Shneider, M.M. / Plattner, M. / Schwarzer, D.

Citation

Journal: To Be Published
Title: Crystal structure of the colanidase tailspike protein gp150 of Phage Phi92 complexed with one repeating unit of colanic acid
Authors: Browning, C. / Plattner, M. / Shneider, M.M. / Gerardy-Schahn, R. / Leiman, P.G. / Schwarzer, D.

History

Deposition	Jul 7, 2018	Deposition site: RCSB / Processing site: RCSB
Supersession	Jul 17, 2019	ID: 4RMX
Revision 1.0	Jul 17, 2019	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6e0v.cif.gz	1 MB	Display	PDBx/mmCIF format
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Validation report

Summary document	6e0v_validation.pdf.gz	484.4 KB	Display	wwPDB validaton report
Full document	6e0v_full_validation.pdf.gz	495.3 KB	Display
Data in XML	6e0v_validation.xml.gz	89.7 KB	Display
Data in CIF	6e0v_validation.cif.gz	143.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/e0/6e0v ftp://data.pdbj.org/pub/pdb/validation_reports/e0/6e0v	HTTPS FTP

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Related structure data

Related structure data	6e0wC 4rmx PDB Unreleased entryS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6e0w-2 6e0w-1 1nd6-d 1tyx-1 2zus-1 2zuu-2 6ssp-1 11223 Search similar-shape structures by Omokage search (details) 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
Related items in Molecule of the Month	#167 - Nov 2013 SNARE Proteins similarity (1)

Deposited unit

A: Bacteriophage Phi92 gp150

B: Bacteriophage Phi92 gp150

C: Bacteriophage Phi92 gp150

hetero molecules

206 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Bacteriophage Phi92 gp150

hetero molecules

A: Bacteriophage Phi92 gp150

hetero molecules

A: Bacteriophage Phi92 gp150

hetero molecules

defined by software
Evidence: gel filtration
206 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Bacteriophage Phi92 gp150

hetero molecules

B: Bacteriophage Phi92 gp150

hetero molecules

B: Bacteriophage Phi92 gp150

hetero molecules

defined by software
206 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Bacteriophage Phi92 gp150

hetero molecules

C: Bacteriophage Phi92 gp150

hetero molecules

C: Bacteriophage Phi92 gp150

hetero molecules

defined by software
206 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	118.400, 118.400, 140.166
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	143
Space group name H-M	P3

Components on special symmetry positions

ID	Model	Components
1	1	A-901- SR
2	1	A-909- CL
3	1	B-901- SR
4	1	B-910- CL
5	1	C-901- SR
6	1	C-909- CL
7	1	A-1150- HOH
8	1	A-1293- HOH
9	1	A-1391- HOH
10	1	A-1392- HOH
11	1	A-1433- HOH
12	1	A-1480- HOH
13	1	A-1499- HOH
14	1	A-1596- HOH
15	1	A-1637- HOH
16	1	A-1658- HOH
17	1	A-1932- HOH
18	1	A-1954- HOH
19	1	B-1053- HOH
20	1	B-1154- HOH
21	1	B-1273- HOH
22	1	B-1428- HOH
23	1	B-1446- HOH
24	1	B-1460- HOH
25	1	B-1475- HOH
26	1	B-1532- HOH
27	1	B-1568- HOH
28	1	B-1584- HOH
29	1	B-1883- HOH
30	1	B-1889- HOH
31	1	B-1896- HOH
32	1	C-1162- HOH
33	1	C-1310- HOH
34	1	C-1321- HOH
35	1	C-1352- HOH
36	1	C-1512- HOH
37	1	C-1637- HOH
38	1	C-1648- HOH
39	1	C-1728- HOH

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Protein , 1 types, 3 molecules ABC

#1: Protein	Bacteriophage Phi92 gp150 Mass: 67382.773 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage phi92 (virus) / Gene: PHI92_gene_150, PHI92_150 / Plasmid: pTSL / Production host: Escherichia coli (E. coli) / Strain (production host): B834/DE3 / References: UniProt: I7I026

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Non-polymers , 5 types, 2672 molecules

#2: Chemical	... ChemComp-SR / STRONTIUM ION Mass: 87.620 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Sr
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2623 / 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: 2.92 Å³/Da / Density % sol: 57.87 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion / pH: 6 / Details: 10% PEG 8000, 0.2M SrCl2, 0.1M MES pH 6.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.7679 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.7679 Å / Relative weight: 1
Reflection	Resolution: 1.75→50 Å / Num. obs: 443661 / % possible obs: 99.7 % / Redundancy: 5.1 % / CC_1/2: 0.999 / R_merge(I) obs: 0.09 / R_rim(I) all: 0.101 / Net I/σ(I): 15.16
Reflection shell	Resolution: 1.75→1.85 Å / Redundancy: 4.8 % / R_merge(I) obs: 0.868 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 70838 / CC_1/2: 0.685 / R_rim(I) all: 0.975 / % possible all: 98.3

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Processing

Software

Name	Version	Classification
PHENIX	(dev_3092: ???)	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4RMX

4rmx
PDB Unreleased entry

Resolution: 1.75→48.149 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 16.05

	R_factor	Num. reflection	% reflection
R_free	0.1625	8867	2 %
R_work	0.1339	-	-
obs	0.1345	443591	99.69 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 18.74 Å²

Refinement step

Cycle: LAST / Resolution: 1.75→48.149 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13695	0	113	2623	16431

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	14242
X-RAY DIFFRACTION	f_angle_d	0.93	19373
X-RAY DIFFRACTION	f_dihedral_angle_d	9.434	8257
X-RAY DIFFRACTION	f_chiral_restr	0.064	2150
X-RAY DIFFRACTION	f_plane_restr	0.006	2538

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 (%)
1.7479-1.7678	0.3258	272	0.2799	13412	X-RAY DIFFRACTION	92
1.7678-1.7886	0.2607	296	0.2343	14521	X-RAY DIFFRACTION	100
1.7886-1.8104	0.2612	293	0.2282	14373	X-RAY DIFFRACTION	100
1.8104-1.8333	0.2591	296	0.2167	14565	X-RAY DIFFRACTION	100
1.8333-1.8574	0.2285	298	0.2055	14563	X-RAY DIFFRACTION	100
1.8574-1.8829	0.2193	298	0.2034	14546	X-RAY DIFFRACTION	100
1.8829-1.9098	0.2343	298	0.1861	14646	X-RAY DIFFRACTION	100
1.9098-1.9383	0.188	296	0.1702	14490	X-RAY DIFFRACTION	100
1.9383-1.9686	0.1828	294	0.157	14446	X-RAY DIFFRACTION	100
1.9686-2.0009	0.1691	295	0.1493	14513	X-RAY DIFFRACTION	100
2.0009-2.0354	0.1612	298	0.1408	14603	X-RAY DIFFRACTION	100
2.0354-2.0724	0.1768	296	0.1385	14486	X-RAY DIFFRACTION	100
2.0724-2.1122	0.1685	300	0.1373	14632	X-RAY DIFFRACTION	100
2.1122-2.1553	0.1532	296	0.1309	14578	X-RAY DIFFRACTION	100
2.1553-2.2022	0.1618	294	0.1243	14414	X-RAY DIFFRACTION	100
2.2022-2.2534	0.1443	298	0.1238	14594	X-RAY DIFFRACTION	100
2.2534-2.3098	0.1643	294	0.1261	14386	X-RAY DIFFRACTION	100
2.3098-2.3722	0.1666	298	0.1234	14566	X-RAY DIFFRACTION	100
2.3722-2.442	0.1755	298	0.1278	14562	X-RAY DIFFRACTION	100
2.442-2.5209	0.1487	296	0.1203	14596	X-RAY DIFFRACTION	100
2.5209-2.611	0.1588	297	0.1187	14512	X-RAY DIFFRACTION	100
2.611-2.7155	0.1475	294	0.1143	14422	X-RAY DIFFRACTION	100
2.7155-2.8391	0.1414	296	0.1142	14577	X-RAY DIFFRACTION	100
2.8391-2.9887	0.1513	296	0.114	14519	X-RAY DIFFRACTION	100
2.9887-3.1759	0.1411	296	0.1136	14521	X-RAY DIFFRACTION	100
3.1759-3.4211	0.1285	296	0.1147	14504	X-RAY DIFFRACTION	100
3.4211-3.7653	0.133	298	0.1122	14596	X-RAY DIFFRACTION	100
3.7653-4.3098	0.1341	298	0.1078	14553	X-RAY DIFFRACTION	100
4.3098-5.4287	0.1273	296	0.1053	14478	X-RAY DIFFRACTION	100
5.4287-48.1671	0.2304	296	0.1916	14550	X-RAY DIFFRACTION	100

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	0.0808	0.0348	-0.1055	0.0717	-0.0721	0.1333	-0.0262	-0.2591	0.0934	0.2733	-0.05	-0.1966	-0.0906	0.0262	-0.0276	0.3305	-0.0059	-0.0416	0.3046	-0.0284	0.1559	62.4463	-25.4722	-14.4471
2	0.1651	0.0254	-0.0001	0.1967	-0.071	0.1819	-0.0035	-0.0367	0.0445	0.0556	0.0025	-0.0063	-0.0382	0.0186	-0	0.1352	-0.0035	-0.0018	0.1204	-0.0219	0.1308	59.3711	-16.9508	-48.4791
3	0.0236	-0.0002	0.0064	0.0466	-0.0345	0.0621	-0.0329	-0.0406	0.0506	-0.0205	0.0199	0.0336	-0.0483	-0.0344	-0	0.1407	-0.0066	-0.0033	0.1243	-0.0123	0.1572	55.0958	-13.6708	-70.0267
4	0.13	0.0266	-0.0304	0.1838	0.1391	0.2041	0.0126	-0.0005	0.0456	-0.0177	0.0041	0.0114	-0.0058	-0.0051	0	0.1106	-0.0063	0.0051	0.1128	0.0015	0.1121	58.748	-18.8222	-86.3778
5	0.186	-0.1352	0.0858	0.1183	0.0312	0.1614	0.0247	0.0402	0.015	-0.1264	-0.0149	0.0292	-0.1308	-0.0254	0.0012	0.164	0.0099	-0.0217	0.1717	0.0141	0.1437	35.3252	-24.1282	-104.6023
6	0.2279	-0.1236	0.152	0.0953	-0.0306	0.212	0.0072	-0.1122	-0.0061	-0.0096	-0.0114	0.0666	-0.0597	0.0067	-0.0064	0.2401	0.0205	-0.0506	0.189	-0.0184	0.1474	11.9841	0.239	-89.4469
7	0.2096	-0.0405	-0.0065	0.3954	-0.0402	0.6176	-0.0367	0.0108	0.049	0.0771	-0.007	-0.1162	-0.0828	0.0932	-0.0225	0.1289	-0.0023	-0.029	0.1018	0.01	0.137	17.1646	4.0378	-132.1702
8	0.2484	-0.0134	-0.1243	0.1265	-0.0626	0.0911	-0.0038	0.1007	0.0472	-0.1336	0.0314	-0.0039	-0.048	0.0316	0.0012	0.2201	-0.003	-0.0017	0.1735	0.0373	0.172	7.5967	19.4627	-171.5564
9	0.0911	0.0755	-0.0441	0.0993	0.0284	0.101	0.0393	-0.268	0.1392	0.0958	-0.0624	0.0306	-0.2086	-0.0619	-0.0348	0.6964	0.1392	0.0072	0.5256	-0.07	0.0028	48.8409	38.8915	8.8048
10	0.1727	-0.1018	-0.0192	0.0655	-0.0778	0.1741	-0.1034	-0.1474	0.1154	0.3936	0.0923	-0.0666	-0.1362	-0.0462	-0.015	0.3948	0.0463	-0.0304	0.2003	-0.0078	0.1656	42.2435	39.0273	-16.7644
11	0.2044	-0.0177	-0.1267	0.2343	-0.0228	0.5215	-0.0065	0.0148	-0.0149	0.0253	0.0059	0.0084	0.0082	-0.072	-0.0047	0.0793	0.011	-0.0107	0.0868	0.0107	0.166	41.7886	36.5656	-49.2721
12	0.0893	-0.0977	0.1118	0.3432	-0.1147	0.1899	-0.0365	0.1781	0.0239	-0.0365	0.239	0.4693	0.0488	-0.1899	0.0094	0.2084	-0.011	-0.0183	0.1961	0.0403	0.3563	43.6887	13.2618	-77.8772

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 201 through 261 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 262 through 491 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 492 through 532 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 533 through 675 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 676 through 802 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 201 through 300 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 301 through 632 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 633 through 802 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 201 through 285 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 286 through 410 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 411 through 675 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 676 through 802 )

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