PDB-8oim: Crystal structure of the lipase SpL from Sphingomonas sp. HXN-200

ID or keywords:

Entry

Database: PDB / ID: 8oim

Title

Crystal structure of the lipase SpL from Sphingomonas sp. HXN-200

Components

Lipase

Keywords

HYDROLASE / alpha-beta hydrolase / lipase / SpL

Function / homology

Lipase, GDXG, putative serine active site / Lipolytic enzymes "G-D-X-G" family, putative serine active site. / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold / hydrolase activity / Lipase

Function and homology information

Biological species

Sphingomonas sp. (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.994 Å

Authors

Mokos, D. / Gruber, K. / Daniel, B.

Funding support

Austria, 2items

Citation

Journal: Acs Catalysis / Year: 2024
Title: Biocatalytic Heteroaromatic Amide Formation in Water Enabled by a Catalytic Tetrad and Two Access Tunnels.
Authors: Zukic, E. / Mokos, D. / Weber, M. / Stix, N. / Ditrich, K. / Ferrario, V. / Muller, H. / Willrodt, C. / Gruber, K. / Daniel, B. / Kroutil, W.

History

Deposition	Mar 23, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 3, 2024	Provider: repository / Type: Initial release
Revision 1.1	Jan 15, 2025	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_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	8oim.cif.gz	244.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8oim.ent.gz	190.1 KB	Display	PDB format
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Validation report

Summary document	8oim_validation.pdf.gz	432.9 KB	Display	wwPDB validaton report
Full document	8oim_full_validation.pdf.gz	436.2 KB	Display
Data in XML	8oim_validation.xml.gz	26.4 KB	Display
Data in CIF	8oim_validation.cif.gz	39.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oi/8oim ftp://data.pdbj.org/pub/pdb/validation_reports/oi/8oim	HTTPS FTP

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Related structure data

Related structure data	8p7eC 8p8fC 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

B: Lipase

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	60.812, 88.966, 65.627
Angle α, β, γ (deg.)	90.000, 96.411, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ALA / End label comp-ID: ALA / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 6 - 314 / Label seq-ID: 20 - 328

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

#1: Protein	Lipase Mass: 35488.051 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphingomonas sp. (bacteria) / Gene: LH19_08550 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0N7I173
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.49 Å³/Da / Density % sol: 50.63 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 5 mg/ml SPL, Index screen condition 78 (0.2 M Ammonium acetate, 0.1 M BIS-TRIS, 25% PEG 3350)

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

PETRA III, DESY

/ Beamline: P11 / Wavelength: 1.03321 Å

Detector

Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 8, 2021

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.03321 Å / Relative weight: 1

Reflection

Resolution: 1.99→42.05 Å / Num. obs: 44854 / % possible obs: 94.9 % / Redundancy: 3.4 % / CC_1/2: 0.992 / R_merge(I) obs: 0.071 / R_pim(I) all: 0.068 / R_rim(I) all: 0.099 / Net I/σ(I): 9.5

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all
8.92-42.05	3.3	0.053	549	0.988	0.052	0.074
1.99-2.05	3.4	0.281	3110	0.925	0.273	0.392

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0403	refinement
Aimless		data scaling
XDS		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.994→42.048 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.948 / SU B: 3.699 / SU ML: 0.102 / Cross valid method: FREE R-VALUE / ESU R: 0.162 / ESU R Free: 0.144
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2017	2309	5.153 %
R_work	0.1647	42496	-
all	0.167	-	-
obs	-	44805	94.571 %

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: 30.462 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.029 Å²	-0 Å²	0.507 Å²
2-	-	1.902 Å²	-0 Å²
3-	-	-	-0.962 Å²

Refinement step

Cycle: LAST / Resolution: 1.994→42.048 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4674	0	0	360	5034

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.012	4798
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	4476
X-RAY DIFFRACTION	r_angle_refined_deg	2.037	1.658	6560
X-RAY DIFFRACTION	r_angle_other_deg	0.641	1.568	10326
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.966	5	616
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.198	5	38
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.415	10	704
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.943	10	206
X-RAY DIFFRACTION	r_chiral_restr	0.106	0.2	722
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	5716
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1036
X-RAY DIFFRACTION	r_nbd_refined	0.214	0.2	1006
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.198	0.2	4185
X-RAY DIFFRACTION	r_nbtor_refined	0.184	0.2	2369
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	2504
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.184	0.2	304
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.021	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.057	0.2	1
X-RAY DIFFRACTION	r_nbd_other	0.138	0.2	23
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.162	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	3.776	2.915	2470
X-RAY DIFFRACTION	r_mcbond_other	3.76	2.914	2470
X-RAY DIFFRACTION	r_mcangle_it	4.704	5.214	3084
X-RAY DIFFRACTION	r_mcangle_other	4.705	5.216	3085
X-RAY DIFFRACTION	r_scbond_it	6.051	3.536	2328
X-RAY DIFFRACTION	r_scbond_other	6.05	3.538	2329
X-RAY DIFFRACTION	r_scangle_it	8.644	6.165	3476
X-RAY DIFFRACTION	r_scangle_other	8.643	6.166	3477
X-RAY DIFFRACTION	r_lrange_it	9.53	28.394	5404
X-RAY DIFFRACTION	r_lrange_other	9.493	28.006	5327
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.088	0.05	9813

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.08757	0.05008
1	2	A	X-RAY DIFFRACTION	Local ncs	0.08757	0.05008

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
1.994-2.046	0.264	157	0.212	2941	0.215	3474	0.954	0.968	89.1767	0.195
2.046-2.102	0.262	139	0.198	3139	0.2	3397	0.958	0.971	96.4969	0.181
2.102-2.163	0.246	162	0.185	3026	0.188	3307	0.958	0.976	96.4016	0.169
2.163-2.229	0.238	158	0.197	2907	0.199	3205	0.964	0.973	95.6318	0.178
2.229-2.302	0.267	169	0.194	2805	0.198	3100	0.949	0.976	95.9355	0.183
2.302-2.382	0.226	157	0.167	2668	0.17	2990	0.969	0.982	94.4816	0.156
2.382-2.472	0.247	135	0.17	2522	0.174	2926	0.966	0.982	90.8066	0.161
2.472-2.573	0.239	147	0.165	2564	0.169	2802	0.962	0.984	96.7523	0.159
2.573-2.686	0.21	113	0.159	2482	0.161	2694	0.975	0.984	96.3252	0.155
2.686-2.817	0.194	135	0.161	2298	0.163	2542	0.975	0.984	95.712	0.162
2.817-2.969	0.215	125	0.162	2220	0.165	2455	0.971	0.984	95.5193	0.165
2.969-3.148	0.216	119	0.16	2088	0.163	2334	0.971	0.984	94.5587	0.168
3.148-3.364	0.198	99	0.164	1931	0.166	2175	0.979	0.983	93.3333	0.177
3.364-3.631	0.196	98	0.159	1682	0.161	2021	0.98	0.985	88.0752	0.174
3.631-3.975	0.17	109	0.145	1692	0.146	1868	0.983	0.987	96.4133	0.16
3.975-4.439	0.143	71	0.135	1578	0.136	1704	0.988	0.988	96.7723	0.156
4.439-5.116	0.148	68	0.142	1392	0.143	1512	0.982	0.988	96.5608	0.168
5.116-6.243	0.192	68	0.164	1144	0.165	1270	0.982	0.986	95.4331	0.187
6.243-8.733	0.17	51	0.166	864	0.166	1004	0.98	0.982	91.1355	0.196
8.733-42.048	0.204	29	0.206	553	0.206	591	0.976	0.971	98.4772	0.22

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