PDB-8yzo: Crystal structural analysis of PaL mutant L297M

ID or keywords:

Entry

Database: PDB / ID: 8yzo

Title

Crystal structural analysis of PaL mutant L297M

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: 1.769 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
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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PDBx/mmCIF format	8yzo.cif.gz	128.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8yzo.ent.gz	91.6 KB	Display	PDB format
PDBx/mmJSON format	8yzo.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8yzo_validation.pdf.gz	432.9 KB	Display	wwPDB validaton report
Full document	8yzo_full_validation.pdf.gz	435.6 KB	Display
Data in XML	8yzo_validation.xml.gz	25.7 KB	Display
Data in CIF	8yzo_validation.cif.gz	41 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yz/8yzo ftp://data.pdbj.org/pub/pdb/validation_reports/yz/8yzo	HTTPS FTP

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Related structure data

Related structure data	8yznC 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

53 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)	81.754, 104.593, 62.030
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-810- HOH
2	1	A-1013- HOH
3	1	A-1069- HOH
4	1	A-1183- HOH

#1: Protein	Lipase Mass: 52968.285 Da / Num. of mol.: 1 / Mutation: L297M Source method: isolated from a genetically manipulated source Details: L297M / 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.: 638 / 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: 2.27 Å³/Da / Density % sol: 50.87 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: Disodium malonate 0.1 M, pH7.0 , PEG3350 15%

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97916 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 30, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97916 Å / Relative weight: 1
Reflection	Resolution: 1.769→44.72 Å / Num. obs: 52610 / % possible obs: 99.9 % / Redundancy: 13.7 % / R_merge(I) obs: 0.09 / Net I/σ(I): 25
Reflection shell	Resolution: 1.77→1.81 Å / R_merge(I) obs: 0.33 / Num. unique obs: 3822

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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: 1.769→44.72 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.954 / WR_factor R_free: 0.187 / WR_factor R_work: 0.143 / SU B: 1.64 / SU ML: 0.053 / Average fsc free: 0.9811 / Average fsc work: 0.9886 / Cross valid method: FREE R-VALUE / ESU R: 0.089 / ESU R Free: 0.092
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1729	2590	4.928 %
R_work	0.1345	49969	-
all	0.136	-	-
obs	-	52559	99.753 %

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: 16.474 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.761 Å²	-0 Å²	-0 Å²
2-	-	-0.195 Å²	0 Å²
3-	-	-	0.956 Å²

Refinement step

Cycle: LAST / Resolution: 1.769→44.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3741	0	0	638	4379

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.011	3857
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	3620
X-RAY DIFFRACTION	r_angle_refined_deg	1.63	1.634	5283
X-RAY DIFFRACTION	r_angle_other_deg	0.575	1.56	8313
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.417	5	513
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.786	5	23
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.853	10	555
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	17.652	10	153
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	593
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	4652
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	888
X-RAY DIFFRACTION	r_nbd_refined	0.216	0.2	711
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.195	0.2	3345
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.2	1901
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	2169
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.216	0.2	490
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.152	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.224	0.2	11
X-RAY DIFFRACTION	r_nbd_other	0.22	0.2	87
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.258	0.2	54
X-RAY DIFFRACTION	r_mcbond_it	2.235	1.59	2034
X-RAY DIFFRACTION	r_mcbond_other	2.235	1.59	2034
X-RAY DIFFRACTION	r_mcangle_it	3.416	2.85	2544
X-RAY DIFFRACTION	r_mcangle_other	3.416	2.851	2545
X-RAY DIFFRACTION	r_scbond_it	3.664	1.919	1823
X-RAY DIFFRACTION	r_scbond_other	3.664	1.919	1824
X-RAY DIFFRACTION	r_scangle_it	5.327	3.33	2736
X-RAY DIFFRACTION	r_scangle_other	5.326	3.33	2737
X-RAY DIFFRACTION	r_lrange_it	7.636	21.928	4593
X-RAY DIFFRACTION	r_lrange_other	7.286	18.253	4335

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
1.769-1.814	0.2	186	0.148	3539	0.151	3822	0.981	0.988	97.4621	0.124
1.814-1.864	0.194	184	0.147	3549	0.149	3733	0.976	0.987	100	0.128
1.864-1.918	0.172	167	0.145	3459	0.147	3627	0.981	0.987	99.9724	0.129
1.918-1.977	0.186	176	0.134	3386	0.137	3563	0.978	0.988	99.9719	0.125
1.977-2.042	0.179	176	0.136	3267	0.138	3443	0.98	0.989	100	0.128
2.042-2.113	0.168	157	0.131	3147	0.132	3304	0.983	0.99	100	0.128
2.113-2.193	0.172	145	0.127	3077	0.129	3222	0.983	0.99	100	0.122
2.193-2.282	0.183	160	0.13	2955	0.133	3115	0.979	0.989	100	0.13
2.282-2.383	0.162	152	0.123	2816	0.125	2968	0.985	0.99	100	0.126
2.383-2.499	0.169	141	0.129	2715	0.131	2856	0.983	0.989	100	0.133
2.499-2.634	0.169	127	0.12	2588	0.122	2715	0.982	0.991	100	0.128
2.634-2.793	0.144	140	0.132	2422	0.133	2562	0.987	0.989	100	0.144
2.793-2.985	0.178	104	0.131	2338	0.133	2442	0.981	0.989	100	0.146
2.985-3.223	0.157	109	0.133	2155	0.134	2264	0.985	0.989	100	0.157
3.223-3.529	0.177	109	0.146	1992	0.148	2101	0.982	0.987	100	0.173
3.529-3.942	0.184	90	0.134	1831	0.136	1921	0.983	0.989	100	0.163
3.942-4.546	0.165	83	0.118	1618	0.12	1704	0.985	0.991	99.8239	0.148
4.546-5.554	0.147	97	0.127	1353	0.128	1452	0.986	0.991	99.8623	0.161
5.554-7.794	0.181	51	0.173	1115	0.173	1166	0.981	0.984	100	0.212
7.794-44.72	0.253	36	0.173	647	0.177	704	0.935	0.976	97.017	0.233

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