PDB-8yzn: Crystal structural analysis of PaL

ID or keywords:

Entry

Database: PDB / ID: 8yzn

Title

Crystal structural analysis of PaL

Components

Lipase

Keywords

BIOSYNTHETIC PROTEIN / Lipase / Pseudomonas alcaligenes / L-menthol

Function / homology

Function and homology information

triacylglycerol lipase / triacylglycerol lipase activity / dipeptidyl-peptidase activity
Similarity search - Function

Biological species

Pseudomonas alcaligenes (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.799 Å

Authors

Xu, G. / Wu, J.

Funding support

China, 1items

Citation

Journal: Structure / Year: 2024
Title: Crystal structure of lipase from Pseudomonas aeruginosa reveals an unusual catalytic triad conformation.
Authors: Xu, G. / Guo, H. / Yu, Z. / Wang, S. / Shen, D. / Yang, L. / Wu, J. / Chen, B. / Yu, H.

History

Deposition	Apr 7, 2024	Deposition site: PDBJ / Processing site: PDBC
Supersession	Apr 17, 2024	ID: 8JJ7
Revision 1.0	Apr 17, 2024	Provider: repository / Type: Initial release
Revision 1.1	Oct 30, 2024	Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8yzn.cif.gz	125.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8yzn.ent.gz	90.5 KB	Display	PDB format
PDBx/mmJSON format	8yzn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8yzn_validation.pdf.gz	430.9 KB	Display	wwPDB validaton report
Full document	8yzn_full_validation.pdf.gz	432.3 KB	Display
Data in XML	8yzn_validation.xml.gz	24.2 KB	Display
Data in CIF	8yzn_validation.cif.gz	38 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yz/8yzn ftp://data.pdbj.org/pub/pdb/validation_reports/yz/8yzn	HTTPS FTP

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Related structure data

Related structure data	8yzoC C: citing same article (ref.)
Similar structure data	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

Deposited unit

A: Lipase

52.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: native gel electrophoresis

Unit cell

Length a, b, c (Å)	81.774, 104.782, 62.372
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-750- HOH
2	1	A-952- HOH

#1: Protein	Lipase Mass: 52821.137 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas alcaligenes (bacteria) / Gene: lip / Production host: Escherichia coli (E. coli) / References: UniProt: H9MZI2, triacylglycerol lipase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 552 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.29 Å³/Da / Density % sol: 46.7 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: Disodium malonate 0.1 M, pH7.0 , PEG3350 18%

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 10, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97853 Å / Relative weight: 1
Reflection	Resolution: 1.799→24.164 Å / Num. obs: 48967 / % possible obs: 96.99 % / Redundancy: 13.2 % / R_merge(I) obs: 0.08 / Net I/σ(I): 23.8
Reflection shell	Resolution: 1.8→1.84 Å / R_merge(I) obs: 0.47 / Num. unique obs: 49315

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0411	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.799→24.164 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.96 / SU B: 2.087 / SU ML: 0.064 / Cross valid method: FREE R-VALUE / ESU R: 0.101 / ESU R Free: 0.098
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1757	1999	4.082 %
R_work	0.1445	46968	-
all	0.146	-	-
obs	-	48967	96.928 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 18.238 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.711 Å²	-0 Å²	-0 Å²
2-	-	1.125 Å²	-0 Å²
3-	-	-	1.586 Å²

Refinement step

Cycle: LAST / Resolution: 1.799→24.164 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3732	0	0	552	4284

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.011	3835
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	3604
X-RAY DIFFRACTION	r_angle_refined_deg	1.511	1.633	5251
X-RAY DIFFRACTION	r_angle_other_deg	0.519	1.56	8273
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.527	5	508
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.453	5	23
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.545	10	549
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	17.397	10	150
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	591
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	4615
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	881
X-RAY DIFFRACTION	r_nbd_refined	0.218	0.2	693
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.192	0.2	3224
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	1888
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	2129
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.217	0.2	413
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.14	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.164	0.2	8
X-RAY DIFFRACTION	r_nbd_other	0.218	0.2	79
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.169	0.2	37
X-RAY DIFFRACTION	r_mcbond_it	2.244	1.857	2026
X-RAY DIFFRACTION	r_mcbond_other	2.244	1.857	2026
X-RAY DIFFRACTION	r_mcangle_it	3.426	3.328	2533
X-RAY DIFFRACTION	r_mcangle_other	3.426	3.328	2534
X-RAY DIFFRACTION	r_scbond_it	3.159	2.117	1809
X-RAY DIFFRACTION	r_scbond_other	3.158	2.117	1810
X-RAY DIFFRACTION	r_scangle_it	4.696	3.729	2717
X-RAY DIFFRACTION	r_scangle_other	4.695	3.729	2718
X-RAY DIFFRACTION	r_lrange_it	6.603	21.283	4463
X-RAY DIFFRACTION	r_lrange_other	6.437	19.078	4273

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.799-1.845	0.23	140	0.201	3305	0.202	3674	0.963	0.973	93.767	0.182
1.845-1.896	0.176	141	0.166	3322	0.167	3559	0.979	0.981	97.3026	0.143
1.896-1.95	0.229	139	0.163	3262	0.166	3486	0.966	0.981	97.5617	0.14
1.95-2.01	0.162	135	0.14	3187	0.14	3391	0.982	0.987	97.9652	0.122
2.01-2.075	0.191	131	0.144	3056	0.146	3258	0.975	0.986	97.8207	0.126
2.075-2.147	0.189	129	0.146	3026	0.147	3224	0.98	0.987	97.8598	0.129
2.147-2.228	0.187	119	0.136	2815	0.138	3051	0.978	0.988	96.1652	0.12
2.228-2.318	0.159	119	0.135	2787	0.136	2955	0.984	0.988	98.3418	0.121
2.318-2.42	0.177	113	0.131	2658	0.133	2829	0.98	0.989	97.9498	0.119
2.42-2.537	0.199	110	0.131	2579	0.134	2734	0.978	0.989	98.3541	0.12
2.537-2.672	0.169	104	0.133	2445	0.134	2583	0.982	0.989	98.6837	0.124
2.672-2.832	0.215	97	0.147	2267	0.149	2498	0.974	0.986	94.6357	0.139
2.832-3.025	0.18	92	0.139	2173	0.141	2310	0.982	0.988	98.0519	0.135
3.025-3.263	0.16	88	0.145	2065	0.145	2186	0.982	0.987	98.4904	0.145
3.263-3.568	0.184	82	0.157	1896	0.158	2012	0.983	0.986	98.3101	0.16
3.568-3.978	0.169	73	0.148	1721	0.149	1832	0.982	0.987	97.9258	0.156
3.978-4.573	0.142	63	0.122	1483	0.123	1643	0.99	0.991	94.0962	0.133
4.573-5.552	0.138	55	0.131	1315	0.131	1407	0.993	0.992	97.3703	0.144
5.552-7.652	0.186	44	0.176	1021	0.177	1128	0.984	0.984	94.4149	0.194
7.652-24.164	0.127	25	0.154	585	0.153	726	0.988	0.986	84.022	0.173

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