PDB-5fya: Cubic crystal of the native PlpD

ID or keywords:

Entry

Database: PDB / ID: 5fya

Title

Cubic crystal of the native PlpD

Components

PATATIN-LIKE PROTEIN, PLPD

Keywords

HYDROLASE / BACTERIAL SECRETION / PHOSPHOLIPASE / LIPID AFFINITY / INFECTION

Function / homology

Function and homology information

protein secretion by the type V secretion system / lipase activity / lipid catabolic process / cell outer membrane / extracellular region
Similarity search - Function

Biological species

PSEUDOMONAS AERUGINOSA (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.141 Å

Authors

Vinicius da Mata Madeira, P. / Zouhir, S. / Basso, P. / Neves, D. / Laubier, A. / Salacha, R. / Bleves, S. / Faudry, E. / Contreras-Martel, C. / Dessen, A.

Citation

Journal: J.Mol.Biol. / Year: 2016
Title: Structural Basis of Lipid Targeting and Destruction by the Type V Secretion System of Pseudomonas Aeruginosa.
Authors: Da Mata Madeira, P.V. / Zouhir, S. / Basso, P. / Neves, D. / Laubier, A. / Salacha, R. / Bleves, S. / Faudry, E. / Contreras-Martel, C. / Dessen, A.

History

Deposition	Mar 4, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 6, 2016	Provider: repository / Type: Initial release
Revision 1.1	May 11, 2016	Group: Database references
Revision 1.2	Sep 13, 2017	Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3	Jan 10, 2024	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5fya.cif.gz	205.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5fya.ent.gz	167.3 KB	Display	PDB format
PDBx/mmJSON format	5fya.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5fya_validation.pdf.gz	426.9 KB	Display	wwPDB validaton report
Full document	5fya_full_validation.pdf.gz	428.2 KB	Display
Data in XML	5fya_validation.xml.gz	18.9 KB	Display
Data in CIF	5fya_validation.cif.gz	25.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fy/5fya ftp://data.pdbj.org/pub/pdb/validation_reports/fy/5fya	HTTPS FTP

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Related structure data

Related structure data	5fquSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5lcn-2 6ou1-d 7l6p-d 5fqu-d 5g5c-1 5lcn-1 3qmw-2 6pxj-d 1iup-1 2bnd-d 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	#239 - Nov 2019 Phospholipase A2 similarity (1)

Deposited unit

A: PATATIN-LIKE PROTEIN, PLPD

B: PATATIN-LIKE PROTEIN, PLPD

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	145.906, 145.906, 145.906
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	198
Space group name H-M	P2₁3

#1: Protein	PATATIN-LIKE PROTEIN, PLPD Mass: 33912.949 Da / Num. of mol.: 2 Fragment: PASSENGER DOMAIN, PATATIN-LIKE PROTEIN PLPD, RESIDUES 20-33 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PA01 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: Q9HYQ6
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

PATATIN-LIKE PROTEIN, PLPD

Mass: 33912.949 Da / Num. of mol.: 2
Fragment: PASSENGER DOMAIN, PATATIN-LIKE PROTEIN PLPD, RESIDUES 20-33
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PA01 / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: Q9HYQ6

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 76 / 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: 3.8 Å³/Da / Density % sol: 68.5 % / Description: NONE
Crystal grow	Details: 1.4 M MAGNESIUM SULFATE, 0.1M BIS-TRIS PROPANE PH 7.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97625 Å / Relative weight: 1
Reflection	Resolution: 2.14→48.64 Å / Num. obs: 54378 / % possible obs: 95.3 % / Observed criterion σ(I): 2.98 / Redundancy: 5.9 % / B_iso Wilson estimate: 54.4 Å² / R_sym value: 0.02 / Net I/σ(I): 61.6
Reflection shell	Resolution: 2.14→2.27 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 3 / R_sym value: 0.57 / % possible all: 85.4

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FQU

5fqu

Resolution: 2.141→48.635 Å / SU ML: 0.37 / σ(F): 1.35 / Phase error: 30.54 / Stereochemistry target values: ML / Details: RESIDUES 91-127 ARE DISORDERED.

	R_factor	Num. reflection	% reflection
R_free	0.2269	5532	10.27 %
R_work	0.1985	-	-
obs	0.2013	54373	95.29 %

Solvent computation

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

Displacement parameters

B_iso mean: 75 Å²

Refinement step

Cycle: LAST / Resolution: 2.141→48.635 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3781	0	0	76	3857

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	3829
X-RAY DIFFRACTION	f_angle_d	0.787	5196
X-RAY DIFFRACTION	f_dihedral_angle_d	11.553	1419
X-RAY DIFFRACTION	f_chiral_restr	0.054	631
X-RAY DIFFRACTION	f_plane_restr	0.003	676

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 (%)
2.1411-2.1654	0.5063	153	0.4918	1377	X-RAY DIFFRACTION	81
2.1654-2.1909	0.5149	164	0.4902	1441	X-RAY DIFFRACTION	86
2.1909-2.2176	0.4823	167	0.4595	1456	X-RAY DIFFRACTION	86
2.2176-2.2456	0.4754	184	0.4249	1484	X-RAY DIFFRACTION	88
2.2456-2.2752	0.4032	193	0.4185	1506	X-RAY DIFFRACTION	90
2.2752-2.3064	0.4701	168	0.3846	1506	X-RAY DIFFRACTION	90
2.3064-2.3393	0.4432	175	0.3873	1546	X-RAY DIFFRACTION	91
2.3393-2.3742	0.3843	185	0.3526	1571	X-RAY DIFFRACTION	93
2.3742-2.4113	0.3872	165	0.3459	1586	X-RAY DIFFRACTION	94
2.4113-2.4509	0.3454	163	0.3221	1601	X-RAY DIFFRACTION	92
2.4509-2.4931	0.3339	169	0.3117	1619	X-RAY DIFFRACTION	95
2.4931-2.5384	0.3373	176	0.2856	1643	X-RAY DIFFRACTION	96
2.5384-2.5873	0.3146	184	0.2748	1631	X-RAY DIFFRACTION	97
2.5873-2.6401	0.3061	189	0.2632	1618	X-RAY DIFFRACTION	97
2.6401-2.6975	0.2767	178	0.2309	1674	X-RAY DIFFRACTION	97
2.6975-2.7602	0.2519	192	0.2386	1655	X-RAY DIFFRACTION	98
2.7602-2.8292	0.2824	191	0.2215	1680	X-RAY DIFFRACTION	98
2.8292-2.9057	0.23	240	0.2135	1635	X-RAY DIFFRACTION	99
2.9057-2.9912	0.2233	192	0.2117	1667	X-RAY DIFFRACTION	99
2.9912-3.0878	0.2887	175	0.2297	1713	X-RAY DIFFRACTION	99
3.0878-3.1981	0.2954	182	0.2087	1703	X-RAY DIFFRACTION	99
3.1981-3.3261	0.249	209	0.1953	1701	X-RAY DIFFRACTION	99
3.3261-3.4774	0.2243	194	0.1955	1706	X-RAY DIFFRACTION	100
3.4774-3.6607	0.2183	186	0.1771	1715	X-RAY DIFFRACTION	100
3.6607-3.89	0.183	196	0.1711	1695	X-RAY DIFFRACTION	100
3.89-4.1902	0.1869	182	0.1521	1725	X-RAY DIFFRACTION	99
4.1902-4.6116	0.1598	189	0.1361	1715	X-RAY DIFFRACTION	99
4.6116-5.2782	0.1652	170	0.1503	1760	X-RAY DIFFRACTION	99
5.2782-6.6473	0.2144	216	0.1921	1732	X-RAY DIFFRACTION	99
6.6473-48.6479	0.1725	205	0.1676	1780	X-RAY DIFFRACTION	98

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	3.95	0.0546	1.6659	3.8362	-0.0734	3.4693	-0.3308	-0.1577	1.1131	-0.0515	0.086	-0.021	-0.4215	-0.0537	0.2609	0.2964	0.0195	-0.0688	0.6638	-0.0034	0.9202	84.4454	41.5218	72.8108
2	3.9414	0.071	-0.0729	6.6749	-0.1192	4.454	-0.3567	-0.1297	0.9464	0.8911	0.5307	1.0568	-0.5177	-1.6489	-0.3039	0.4204	0.1028	-0.0066	0.939	-0.0768	1.0958	70.4878	40.6543	79.9098
3	3.1877	-1.2158	2.3457	3.8107	-1.2012	2.7316	-0.0246	-0.0173	0.4385	-0.1221	0.0199	0.4335	0.1362	-0.3489	-0.0033	0.2762	-0.0141	-0.0669	0.7457	0.0336	0.6151	75.1667	28.4498	71.2719
4	2.2653	-0.2095	0.9161	4.8869	-2.7978	4.3778	-0.0029	-0.0814	0.142	0.3206	0.2028	-0.2594	-0.0125	0.0361	-0.2512	0.2885	0.074	-0.0344	0.6858	-0.0922	0.5825	86.3686	27.5947	80.2866
5	3.8656	0.9183	1.781	4.019	0.1626	2.4449	-0.0049	-0.2811	1.3701	0.3141	-0.075	-0.0428	-0.4054	-0.096	-0.0004	0.4598	0.0394	-0.0986	0.6798	-0.0936	1.0722	89.0458	45.8334	81.0625
6	2.6171	0.2697	0.8619	3.0311	1.015	5.6156	0.1083	-0.1479	-0.2492	0.1308	0.1235	-0.1432	0.672	0.3657	-0.2205	0.7464	0.0217	-0.0459	0.8162	-0.0116	0.2764	105.9517	0.5498	97.3327
7	7.2558	-0.6747	3.153	2.9809	2.15	6.7695	0.3302	-1.1207	-0.5527	0.5453	0.0434	0.1326	1.8331	-0.4197	-0.2403	1.0961	-0.1428	-0.0126	0.9275	0.1249	0.3696	98.9385	-6.3858	105.9962
8	1.88	-1.8383	1.3006	1.9752	-1.3667	1.0302	-0.1464	-0.9533	0.0497	0.5015	0.6119	0.5669	-0.5539	-1.2111	-0.4788	0.8638	-0.0562	0.1542	1.5556	0.0968	0.61	86.0059	6.705	106.2751
9	4.2162	-1.2486	1.9379	3.6439	-0.5516	3.4734	-0.3765	-0.3235	0.2182	0.3323	0.2733	0.0925	-0.402	0.355	0.052	0.731	-0.101	-0.0773	0.8208	-0.0167	0.3103	99.8522	12.9181	99.7378
10	8.2489	-2.8821	-0.1818	2.0009	0.1366	2.2633	-0.0034	-0.0343	0.0555	-0.3291	0.2573	0.1022	-0.3593	-0.0178	-0.1825	0.7325	-0.0915	0.0325	0.6494	-0.0003	0.381	93.2429	14.5324	86.3406
11	2.9158	1.0163	-1.0092	4.0712	0.2279	3.7588	-0.3111	0.0998	-0.2112	-0.4888	0.1543	-0.0431	0.6649	0.0219	0.1625	0.8277	-0.0247	-0.0582	0.7638	-0.0179	0.3161	102.0244	-3.4035	88.7617

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 23 THROUGH 71 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 72 THROUGH 128 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 129 THROUGH 172 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 173 THROUGH 267 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 268 THROUGH 311 )
6	X-RAY DIFFRACTION	6	CHAIN 'B' AND (RESID 22 THROUGH 70 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 71 THROUGH 84 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 85 THROUGH 144 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 145 THROUGH 244 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 245 THROUGH 267 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 268 THROUGH 312 )

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