PDB-8spk: Crystal structure of Antarctic PET-degrading enzyme

ID or keywords:

Entry

Database: PDB / ID: 8spk

Title

Crystal structure of Antarctic PET-degrading enzyme

Components

Lipase 1

Keywords

HYDROLASE / PET-degrading enzyme / Antarctic

Function / homology

triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / Alpha/Beta hydrolase fold / metal ion binding / MALONATE ION / Lipase 1

Function and homology information

Biological species

Moraxella (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Furtado, A.A. / Blazquez-Sanchez, P. / Grinen, A. / Vargas, J.A. / Leonardo, D.A. / Sculaccio, S.A. / Pereira, H.M. / Diez, B. / Garratt, R.C. / Ramirez-Sarmiento, C.A.

Funding support

Brazil, 1items

Citation

Journal: Protein Sci. / Year: 2023
Title: Engineering the catalytic activity of an Antarctic PET-degrading enzyme by loop exchange.
Authors: Blazquez-Sanchez, P. / Vargas, J.A. / Furtado, A.A. / Grinen, A. / Leonardo, D.A. / Sculaccio, S.A. / Pereira, H.D. / Sonnendecker, C. / Zimmermann, W. / Diez, B. / Garratt, R.C. / Ramirez-Sarmiento, C.A.

History

Deposition	May 3, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 23, 2023	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 2023	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation_author.identifier_ORCID
Revision 1.2	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8spk.cif.gz	230.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8spk.ent.gz	183.2 KB	Display	PDB format
PDBx/mmJSON format	8spk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8spk_validation.pdf.gz	460.1 KB	Display	wwPDB validaton report
Full document	8spk_full_validation.pdf.gz	463.7 KB	Display
Data in XML	8spk_validation.xml.gz	28 KB	Display
Data in CIF	8spk_validation.cif.gz	43.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sp/8spk ftp://data.pdbj.org/pub/pdb/validation_reports/sp/8spk	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Lipase 1

B: Lipase 1

hetero molecules

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

1

A: Lipase 1

hetero molecules

defined by author
Evidence: gel filtration
31.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Lipase 1

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

Unit cell

Length a, b, c (Å)	131.180, 131.180, 131.180
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	198
Space group name H-M	P2₁3

#1: Protein	Lipase 1 / Triacylglycerol lipase Mass: 30939.010 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Moraxella (bacteria) / Gene: lip1, L1 / Plasmid: pET28a-TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P19833, triacylglycerol lipase
#2: Chemical	ChemComp-MLI / MALONATE ION Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₂O₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 672 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.04 Å³/Da / Density % sol: 59.54 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.4 M sodium malonate dibasic monohydrate at pH 7.0

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.9772 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 9, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9772 Å / Relative weight: 1
Reflection	Resolution: 1.6→92.76 Å / Num. obs: 99279 / % possible obs: 100 % / Redundancy: 38.4 % / CC_1/2: 0.999 / R_merge(I) obs: 0.272 / R_pim(I) all: 0.044 / R_rim(I) all: 0.276 / Χ²: 0.96 / Net I/σ(I): 13.3 / Num. measured all: 3811265
Reflection shell	Resolution: 1.6→1.68 Å / % possible obs: 100 % / Redundancy: 39.3 % / R_merge(I) obs: 2.195 / Num. measured all: 565765 / Num. unique obs: 14382 / CC_1/2: 0.813 / R_pim(I) all: 0.354 / R_rim(I) all: 2.224 / Χ²: 0.88 / Net I/σ(I) obs: 2.4

-
Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.6→92.76 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.08 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1797	4908	4.95 %
R_work	0.1532	-	-
obs	0.1544	99232	99.99 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.6→92.76 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4070	0	14	674	4758

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.017	4216
X-RAY DIFFRACTION	f_angle_d	1.501	5724
X-RAY DIFFRACTION	f_dihedral_angle_d	12.079	1552
X-RAY DIFFRACTION	f_chiral_restr	0.104	614
X-RAY DIFFRACTION	f_plane_restr	0.015	747

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 (%)
1.6-1.62	0.2366	163	0.2037	3114	X-RAY DIFFRACTION	100
1.62-1.63	0.2292	174	0.2015	3079	X-RAY DIFFRACTION	100
1.64-1.65	0.2019	166	0.1921	3134	X-RAY DIFFRACTION	100
1.66-1.68	0.2422	196	0.1957	3077	X-RAY DIFFRACTION	100
1.68-1.7	0.2253	167	0.1935	3155	X-RAY DIFFRACTION	100
1.7-1.72	0.2878	162	0.231	3118	X-RAY DIFFRACTION	100
1.72-1.75	0.2606	165	0.2268	3102	X-RAY DIFFRACTION	100
1.75-1.77	0.3075	151	0.2131	3117	X-RAY DIFFRACTION	100
1.77-1.8	0.2126	180	0.2079	3126	X-RAY DIFFRACTION	100
1.8-1.83	0.2194	143	0.1825	3135	X-RAY DIFFRACTION	100
1.83-1.86	0.2172	173	0.1694	3093	X-RAY DIFFRACTION	100
1.86-1.89	0.1897	199	0.1578	3103	X-RAY DIFFRACTION	100
1.89-1.93	0.1918	142	0.1592	3186	X-RAY DIFFRACTION	100
1.93-1.97	0.1985	136	0.1539	3134	X-RAY DIFFRACTION	100
1.97-2.01	0.1856	176	0.1562	3107	X-RAY DIFFRACTION	100
2.01-2.06	0.1828	159	0.1546	3135	X-RAY DIFFRACTION	100
2.06-2.11	0.1787	163	0.1572	3145	X-RAY DIFFRACTION	100
2.11-2.17	0.1809	145	0.1608	3102	X-RAY DIFFRACTION	100
2.17-2.23	0.1775	171	0.1567	3170	X-RAY DIFFRACTION	100
2.23-2.3	0.1776	152	0.145	3152	X-RAY DIFFRACTION	100
2.3-2.39	0.1631	153	0.1383	3157	X-RAY DIFFRACTION	100
2.39-2.48	0.1695	166	0.1419	3125	X-RAY DIFFRACTION	100
2.48-2.6	0.1797	179	0.1504	3131	X-RAY DIFFRACTION	100
2.6-2.73	0.1548	178	0.1484	3174	X-RAY DIFFRACTION	100
2.73-2.9	0.1647	149	0.153	3164	X-RAY DIFFRACTION	100
2.9-3.13	0.1693	168	0.1513	3156	X-RAY DIFFRACTION	100
3.13-3.44	0.1912	146	0.1347	3188	X-RAY DIFFRACTION	100
3.44-3.94	0.1396	151	0.1223	3202	X-RAY DIFFRACTION	100
3.94-4.96	0.1268	149	0.1129	3228	X-RAY DIFFRACTION	100
4.97-92.76	0.1735	186	0.166	3315	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	0.7207	0.7417	-0.2808	5.9475	0.6641	0.5824	-0.2508	-0.0095	-0.3795	0.0953	0.0119	-0.1584	0.7746	0.0702	-0.1044	0.3174	0.0377	0.0495	0.2154	-0.0241	0.168	39.901	-21.914	5.548
2	1.1412	-0.4609	-1.4324	0.5489	1.2232	4.2982	-0.0131	-0.3665	0.138	0.0761	0.1458	-0.0949	-0.2576	0.5641	-0.3514	0.1914	0.0183	-0.0091	0.216	-0.0234	0.1384	52.159	-23.012	-11.796
3	1.2972	-0.1904	-0.5135	0.8765	0.1967	1.4608	-0.069	-0.0871	-0.052	0.0972	0.0318	0.0079	0.1236	0.0641	0.0286	0.1257	0.006	0.0104	0.0837	-0.0041	0.0772	41.555	-24.66	-16.335
4	2.0328	0.8828	-0.7727	2.7932	-0.4953	3.3629	-0.0105	0.0496	0.0766	-0.0633	-0.0016	0.0238	-0.1327	-0.2064	-0.0163	0.107	0.0217	0.0044	0.0985	-0.0199	0.0909	27.443	-12.477	-18.657
5	0.6043	-0.1066	-0.5273	1.4379	-0.5934	2.2949	-0.022	-0.0598	0.0271	0.0841	0.0245	0.0309	-0.0573	0.0269	0.0008	0.1483	0.004	0.0032	0.125	-0.0169	0.1058	32.846	-13.5	-6.606
6	1.2875	-0.3249	-0.4949	0.4815	1.4263	4.7021	-0.3658	0.1534	0.3891	-0.449	-0.0534	-0.2422	-0.3037	-0.4367	-0.0006	0.3351	0.0048	0.0035	0.1395	0.0112	0.2613	41.929	24.198	-44.238
7	1.457	0.5803	0.3295	4.8352	1.0787	0.4874	-0.0132	-0.1047	0.1798	0.1933	-0.0643	0.4437	-0.0874	-0.1092	0.1848	0.138	0.0189	0.0006	0.1397	-0.0042	0.0989	30.497	5.898	-45.024
8	1.1176	-0.1757	0.0124	1.9082	0.296	1.1133	0.0074	-0.028	0.0629	0.0101	-0.0136	0.0483	-0.1289	-0.0702	-0.0116	0.0673	-0.0009	-0.0034	0.0829	-0.0059	0.0512	37.177	2.754	-44.312
9	3.1725	1.0832	1.8624	7.3355	0.0096	5.4069	0.1219	0.2042	0.2764	-0.0626	-0.1415	0.2653	-0.1867	-0.2207	0.0636	0.1649	0.0186	-0.0015	0.1322	0.0049	0.0536	36.583	8.481	-57.246
10	1.3567	-0.5141	0.3097	2.5571	-1.2014	2.9255	-0.0082	0.0596	-0.0288	-0.117	-0.0118	-0.1438	0.115	0.0799	0.0236	0.096	-0.0129	0.0018	0.0814	-0.0108	0.091	50.231	-0.788	-43.224
11	2.0551	0.6775	-1.2118	1.8476	-0.2965	2.426	0.0376	-0.0699	0.0054	0.2118	-0.0004	-0.0394	0.0642	-0.0823	-0.0181	0.1045	-0.0132	-0.0185	0.0819	-0.0187	0.0735	50.779	2.098	-30.53
12	1.179	0.2759	0.3154	1.0445	-0.1836	1.9161	0.0021	-0.0243	0.1755	-0.0118	-0.0335	0.0153	-0.1576	-0.0075	0.0395	0.1324	0.0007	0.0042	0.0947	-0.0168	0.1474	50.619	15.992	-36.539

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 55:71 )	A	55 - 71
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 72:97 )	A	72 - 97
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 98:225 )	A	98 - 225
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 226:259 )	A	226 - 259
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 260:319 )	A	260 - 319
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 56:71 )	B	56 - 71
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 72:97 )	B	72 - 97
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 98:169 )	B	98 - 169
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 170:182 )	B	170 - 182
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 183:225 )	B	183 - 225
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 226:272 )	B	226 - 272
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 273:319 )	B	273 - 319

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi