PDB-2y6v: Peroxisomal alpha-beta-hydrolase Lpx1 (Yor084w) from Saccharomyce...

ID or keywords:

Entry

Database: PDB / ID: 2y6v

Title

Peroxisomal alpha-beta-hydrolase Lpx1 (Yor084w) from Saccharomyces cerevisiae (crystal form I)

Components

PEROXISOMAL MEMBRANE PROTEIN LPX1

Keywords

HYDROLASE / PUTATIVE ESTERASE / PUTATIVE LIPASE

Function / homology

Function and homology information

triglyceride catabolic process / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / triacylglycerol lipase activity / peroxisomal matrix
Similarity search - Function

Biological species

SACCHAROMYCES CEREVISIAE (brewer's yeast)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.83 Å

Authors

Thoms, S. / Niemann, H.H.

Citation

Journal: J.Struct.Biol. / Year: 2011
Title: The Unusual Extended C-Terminal Helix of the Peroxisomal Alpha-Beta-Hydrolase Lpx1 is Involved in Dimer Contacts But Dispensable for Dimerization
Authors: Thoms, S. / Hofhuis, J. / Thoing, C. / Gartner, J. / Niemann, H.H.

History

Deposition	Jan 26, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 13, 2011	Provider: repository / Type: Initial release
Revision 1.1	Aug 17, 2011	Group: Database references
Revision 1.2	Jan 22, 2014	Group: Data collection / Version format compliance
Revision 1.3	May 8, 2019	Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol / struct_conn Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4	May 1, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2y6v.cif.gz	443.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2y6v.ent.gz	370.2 KB	Display	PDB format
PDBx/mmJSON format	2y6v.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y6/2y6v ftp://data.pdbj.org/pub/pdb/validation_reports/y6/2y6v	HTTPS FTP

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Related structure data

Related structure data	2y6uC C: citing same article (ref.)
Similar structure data	2yxx-2 1hkw-d 6f30-2 3n29-d 6f2y-2 6f33-1 6f2t-2 6n2f-d 1htt-2 6f2t-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#165 - Sep 2013 Designed Protein Cages similarity (1) #220 - Apr 2018 Dehalogenases similarity (1)

Deposited unit

A: PEROXISOMAL MEMBRANE PROTEIN LPX1

B: PEROXISOMAL MEMBRANE PROTEIN LPX1

C: PEROXISOMAL MEMBRANE PROTEIN LPX1

hetero molecules

136 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: PEROXISOMAL MEMBRANE PROTEIN LPX1

B: PEROXISOMAL MEMBRANE PROTEIN LPX1

hetero molecules

defined by author&software
90.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: PEROXISOMAL MEMBRANE PROTEIN LPX1

hetero molecules

C: PEROXISOMAL MEMBRANE PROTEIN LPX1

hetero molecules

defined by author&software
90.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	140.480, 87.770, 125.040
Angle α, β, γ (deg.)	90.00, 95.10, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	B
2	1	A
1	2	C
2	2	A

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	B	1 - 381
2	1	1	1	A	1 - 381
1	1	2	1	C	1 - 44
2	1	2	1	A	1 - 44
1	2	2	1	C	52 - 77
2	2	2	1	A	52 - 77
1	3	2	1	C	85 - 132
2	3	2	1	A	85 - 132
1	4	2	1	C	134 - 173
2	4	2	1	A	134 - 173
1	5	2	1	C	186 - 205
2	5	2	1	A	186 - 205
1	6	2	1	C	209 - 344
2	6	2	1	A	209 - 344
1	7	2	1	C	358 - 381
2	7	2	1	A	358 - 381

NCS ensembles :

ID
1
2

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.7361, 0.3666, 0.569), (0.3673, -0.4896, 0.7908), (0.5685, 0.7911, 0.2257)	126.3, 32.1, -79.37
2	given	(0.709, 0.4021, -0.5794), (-0.349, -0.5138, -0.7837), (-0.6128, 0.7578, -0.2239)	-10.21, 174, 81.13

#1: Protein	PEROXISOMAL MEMBRANE PROTEIN LPX1 / LIPASE OF PEROXISOMES PROTEIN 1 / LPX1-YOR084W Mass: 45208.359 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: PST281 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): CODONPLUS RIL References: UniProt: Q12405, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y
Sequence details	C-TERMINAL ELEVEN RESIDUES ARE CLONING ARTEFACT (AAALE) AND HEXA-HISTIDINE TAG.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.9 Å³/Da / Density % sol: 58 % / Description: NONE
Crystal grow	Temperature: 293 K / Method: vapor diffusion Details: HANGING OR SITTING DROP VAPOR DIFFUSION AT 20 DEGREES CELSIUS. 4 UL OF PROTEIN (7.9 MG/ML) MIXED WITH 2UL RESERVOIR (0.1 M HEPES, PH 7.5, 10 % PEG 8000).

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
Detector	Type: RIGAKU CCD / Detector: CCD / Date: Sep 3, 2008 / Details: VARIMAX HF CONFOCAL
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.83→20 Å / Num. obs: 34876 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / B_iso Wilson estimate: 36.5 Å² / R_merge(I) obs: 0.09 / Net I/σ(I): 15
Reflection shell	Resolution: 2.83→2.9 Å / Redundancy: 2.4 % / R_merge(I) obs: 0.4 / Mean I/σ(I) obs: 2.97 / % possible all: 68.4

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0109	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: ENSEMBLE OF TEN ALPHA-BETA HYDROLASES AS POLY-ALA MODELS TRIMMED TO THE COMMON CORE.

Resolution: 2.83→19.75 Å / Cor.coef. F_o:F_c: 0.914 / Cor.coef. F_o:F_c free: 0.875 / SU B: 30.988 / SU ML: 0.283 / Cross valid method: THROUGHOUT / ESU R Free: 0.378 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25408	1744	5 %	RANDOM
R_work	0.20707	-	-	-
obs	0.20938	33131	100 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 32.557 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.19 Å²	0 Å²	0.24 Å²
2-	-	-0.35 Å²	0 Å²
3-	-	-	0.2 Å²

Refinement step

Cycle: LAST / Resolution: 2.83→19.75 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8786	0	15	71	8872

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	8995
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	6131
X-RAY DIFFRACTION	r_angle_refined_deg	1.475	1.95	12184
X-RAY DIFFRACTION	r_angle_other_deg	0.967	3	14897
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	18.628	5.234	1112
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.289	23.58	433
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.396	15	1522
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.662	15	72
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	1367
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	9886
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1838
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.304	1.5	5478
X-RAY DIFFRACTION	r_mcbond_other	0.143	1.5	2187
X-RAY DIFFRACTION	r_mcangle_it	0.553	2	8883
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.913	3	3517
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.294	4.5	3301
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	B	4836	tight positional	0.04	0.05
1	2	A	4836	tight positional	0.04	0.05
2	1	C	4410	tight positional	0.05	0.05
2	2	A	4410	tight positional	0.05	0.05
1	1	B	4836	tight thermal	0.1	0.5
1	2	A	4836	tight thermal	0.1	0.5
2	1	C	4410	tight thermal	0.11	0.5
2	2	A	4410	tight thermal	0.11	0.5

LS refinement shell

Resolution: 2.827→2.899 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.35	89	-
R_work	0.263	1700	-
obs	-	-	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	2.6004	-0.7972	0.0227	1.9342	-0.1965	2.2969	-0.0345	0.1166	-0.1937	-0.0867	0.1073	-0.0505	0.2139	0.1512	-0.0728	0.0816	-0.0004	0.0308	0.03	-0.0269	0.0397	103.9396	52.3618	15.264
2	1.5672	-0.5281	-0.8079	1.4218	0.5656	2.5571	0.0537	0.3689	0.2752	-0.3358	-0.0085	-0.3664	-0.2697	0.3023	-0.0452	0.1653	-0.0416	0.056	0.2375	0.0197	0.2105	114.5842	64.7537	8.1668
3	5.1456	0.0445	-0.519	2.6621	1.8026	3.1682	-0.0915	-0.2262	0.0157	0.3481	0.1233	-0.2951	0.1572	0.4749	-0.0318	0.1151	0.0653	-0.0786	0.148	-0.009	0.0921	117.1126	53.047	27.5857
4	4.617	-0.1119	0.2915	5.5974	0.9551	0.6893	-0.2314	0.1902	-0.2219	0.2989	0.408	-0.4366	0.3249	0.4093	-0.1766	0.4099	0.1159	-0.0241	0.3449	0.0096	0.2667	84.8551	34.0038	38.3006
5	2.5514	-0.0872	-0.408	3.1746	0.0162	1.4233	-0.0471	0.132	0.0924	-0.2554	0.0541	0.2387	0.0007	-0.2973	-0.007	0.0901	-0.0152	0.0219	0.0654	0.0016	0.0525	77.3129	57.3052	23.9902
6	2.6444	0.3843	0.314	0.8462	-0.0395	0.7458	0.0445	-0.363	-0.3087	0.2145	0.0326	0.2674	0.187	-0.3505	-0.0771	0.2002	-0.045	0.0612	0.2048	0.0516	0.2109	70.2722	48.9503	38.8368
7	6.1478	0.5026	0.3251	2.6741	0.0154	4.0829	0.0098	-0.3132	0.3399	0.2433	-0.0036	0.2909	-0.2932	-0.0953	-0.0063	0.1524	0.0484	0.0435	0.0562	-0.0514	0.1291	75.2475	70.9643	35.4114
8	2.313	-1.9909	0.3421	2.1213	0.2432	4.9918	-0.2101	0.1674	0.1949	0.0116	-0.1483	0.2022	-0.2539	-0.6032	0.3584	0.3731	-0.051	-0.0174	0.1824	0.0578	0.4476	97.1969	76.6211	4.1669
9	1.3204	0.2994	-0.2861	1.241	0.1554	2.1657	-0.076	0.1425	0.1945	-0.1315	-0.0347	-0.0019	-0.2197	-0.022	0.1107	0.0503	-0.0064	0.0042	0.0199	0.0197	0.1047	74.8513	100.6383	51.8464
10	9.324	-2.9221	-2.533	2.8453	3.1744	11.8778	-0.4622	-0.7356	-0.5502	0.7474	-0.068	0.0393	1.8327	-0.2638	0.5302	0.4735	0.0341	-0.0159	0.4036	0.0896	0.4992	84.6904	76.8405	71.8495
11	2.6845	1.1576	-0.4814	1.8643	-0.2699	1.3343	0.0394	-0.1741	0.0589	0.176	-0.1048	-0.305	-0.0458	0.5126	0.0653	0.0556	-0.01	0.0124	0.1989	0.0386	0.1586	92.2985	94.323	58.1372
12	4.1046	-0.1873	-1.462	3.8773	-0.604	3.2874	0.0886	0.326	-0.4549	-0.2523	-0.0862	0.02	0.2686	0.1034	-0.0024	0.0932	0.0225	0.0226	0.0451	-0.0578	0.1069	78.1544	84.2887	43.3183
13	1.4779	-1.3078	-0.5428	1.3024	0.0396	1.8884	0.0976	0.0509	0.1316	-0.2225	0.0036	-0.0748	0.1287	-0.0748	-0.1012	0.3057	-0.0725	-0.0796	0.2031	-0.0566	0.2131	42.3578	97.7152	45.5689
14	36.0616	18.6686	-9.455	35.7237	7.5015	36.0108	0.6285	-0.3454	-2.5095	0.4726	-0.1701	0.8738	-0.2331	-0.0483	-0.4584	0.301	-0.0603	-0.0761	0.2641	0.0799	0.563	29.7907	71.975	51.3469

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 191
2	X-RAY DIFFRACTION	2	A	192 - 283
3	X-RAY DIFFRACTION	3	A	284 - 348
4	X-RAY DIFFRACTION	4	A	349 - 381
5	X-RAY DIFFRACTION	5	B	3 - 191
6	X-RAY DIFFRACTION	6	B	192 - 283
7	X-RAY DIFFRACTION	7	B	284 - 348
8	X-RAY DIFFRACTION	8	B	349 - 381
9	X-RAY DIFFRACTION	9	C	3 - 174
10	X-RAY DIFFRACTION	10	C	175 - 191
11	X-RAY DIFFRACTION	11	C	192 - 283
12	X-RAY DIFFRACTION	12	C	284 - 348
13	X-RAY DIFFRACTION	13	C	349 - 381
14	X-RAY DIFFRACTION	14	C	382 - 387

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