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- PDB-2y6u: Peroxisomal alpha-beta-hydrolase Lpx1 (Yor084w) from Saccharomyce... -

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Basic information

Entry
Database: PDB / ID: 2y6u
TitlePeroxisomal alpha-beta-hydrolase Lpx1 (Yor084w) from Saccharomyces cerevisiae (crystal form II)
ComponentsPEROXISOMAL MEMBRANE PROTEIN LPX1
KeywordsHYDROLASE / PUTATIVE ESTERASE / PUTATIVE LIPASE
Function / homology
Function and homology information


triglyceride catabolic process / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / triglyceride lipase activity / peroxisomal matrix
Similarity search - Function
Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Peroxisomal membrane protein LPX1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsThoms, S. / Niemann, H.H.
CitationJournal: 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
DepositionJan 26, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2011Group: Database references
Revision 1.2Jul 24, 2019Group: Data collection / Derived calculations
Category: diffrn_source / pdbx_struct_special_symmetry / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Sep 25, 2019Group: Data collection / Experimental preparation / Other / Category: exptl_crystal_grow / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PEROXISOMAL MEMBRANE PROTEIN LPX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3002
Polymers45,2081
Non-polymers921
Water5,044280
1
A: PEROXISOMAL MEMBRANE PROTEIN LPX1
hetero molecules

A: PEROXISOMAL MEMBRANE PROTEIN LPX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,6014
Polymers90,4172
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area6660 Å2
ΔGint-44.4 kcal/mol
Surface area30700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.156, 87.156, 125.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2206-

HOH

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Components

#1: Protein PEROXISOMAL MEMBRANE PROTEIN LPX1 / LIPASE OF PEROXISOMES PROTEIN 1 / LPX1-YOR084W


Mass: 45208.359 Da / Num. of mol.: 1
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): CODON PLUS RIL
References: UniProt: Q12405, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsC-TERMINAL ELEVEN RESIDUES ARE CLONING ARTEFACT (AAALE) AND HEXA-HISTIDINE TAG.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 59 % / Description: NONE
Crystal growMethod: vapor diffusion
Details: VAPOR DIFFUSION. DROP CONTAINED 2.5 UL PROTEIN (2.0 MG/ML), 0.5 UL ADDITIVE (0.1 M UREA) AND 2 UL RESERVOIR (8 % PEG 8000, 0.1 M HEPES, PH 7.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.0332
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 26, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.9→48 Å / Num. obs: 44068 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 10.3 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 18.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.4 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y6V

2y6v


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.91 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.179 2219 5 %RANDOM
Rwork0.15343 ---
obs0.15474 41757 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.025 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2967 0 6 280 3253
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0223163
X-RAY DIFFRACTIONr_bond_other_d0.0010.022164
X-RAY DIFFRACTIONr_angle_refined_deg2.0181.9524318
X-RAY DIFFRACTIONr_angle_other_deg1.08835293
X-RAY DIFFRACTIONr_dihedral_angle_1_deg22.0175.285421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35323.885157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20515543
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8571525
X-RAY DIFFRACTIONr_chiral_restr0.140.2483
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213547
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02646
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2221.51916
X-RAY DIFFRACTIONr_mcbond_other0.3931.5762
X-RAY DIFFRACTIONr_mcangle_it2.0323132
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.93231247
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.3454.51165
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 162 -
Rwork0.196 3006 -
obs--99.84 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
12.17730.36180.52023.65221.3972.31820.03570.0852-0.23810.2079-0.14960.54070.2504-0.37090.11390.0667-0.01440.0060.17060.01250.1665-37.0282-4.46238.7453
22.4550.17190.1293.43971.21153.06690.00050.2213-0.1772-0.0528-0.01260.23720.1391-0.22270.01210.01540.0015-0.01240.1122-0.00430.0496-31.4446-3.51665.3957
31.8989-0.29580.6351.6313-0.24792.8178-0.04320.38740.3271-0.2836-0.0156-0.0553-0.42950.12850.05880.1416-0.00340.00820.15280.02510.1032-21.9596.2272-0.2924
45.35650.8049-0.38073.09150.10026.33970.02580.22780.0133-0.0911-0.0208-0.16050.03740.3792-0.0050.0410.04120.01270.1396-0.05670.0756-10.5905-7.70533.7526
53.31170.4349-0.74853.0491-0.02175.0939-0.06430.4054-0.4264-0.3048-0.0094-0.12520.55810.12240.07370.09480.01790.00560.1771-0.1050.1182-20.173-14.0208-3.5877
61.79672.82580.34254.45780.53230.06890.2662-0.2612-0.25740.1908-0.3356-0.44690.0793-0.04780.06950.9901-0.12870.0351.31190.01661.0034-32.6812-26.002119.866
721.05583.43662.37176.20580.25053.39850.1364-0.02-0.5760.0730.0522-0.00880.3392-0.063-0.18870.2685-0.04510.01640.08210.0930.1929-30.3424-24.73236.9585
830.135-2.43768.37743.4901-5.844910.45151.0868-0.5199-1.7782-0.3553-0.40390.24290.79930.5684-0.68290.51580.0966-0.13260.31410.03020.5725-12.1012-22.902839.6455
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 54
2X-RAY DIFFRACTION2A55 - 137
3X-RAY DIFFRACTION3A138 - 283
4X-RAY DIFFRACTION4A284 - 316
5X-RAY DIFFRACTION5A317 - 348
6X-RAY DIFFRACTION6A349 - 356
7X-RAY DIFFRACTION7A357 - 376
8X-RAY DIFFRACTION8A377 - 381

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