[English] 日本語
Yorodumi
- PDB-2y6u: Peroxisomal alpha-beta-hydrolase Lpx1 (Yor084w) from Saccharomyce... -

+
Open data


ID or keywords:

Loading...

-
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 / triacylglycerol 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
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


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

-
Experimental details

-
Experiment

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

-
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)

-
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

-
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

+
About Yorodumi

-
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

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

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

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

Read more