[English] 日本語
Yorodumi
- PDB-2xpy: Structure of Native Leukotriene A4 Hydrolase from Saccharomyces c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xpy
TitleStructure of Native Leukotriene A4 Hydrolase from Saccharomyces cerevisiae
ComponentsLEUKOTRIENE A-4 HYDROLASE
KeywordsHYDROLASE
Function / homology
Function and homology information


Synthesis of Leukotrienes (LT) and Eoxins (EX) / Biosynthesis of protectins / Biosynthesis of D-series resolvins / Biosynthesis of E-series 18(S)-resolvins / Biosynthesis of aspirin-triggered D-series resolvins / Biosynthesis of E-series 18(R)-resolvins / cellular lipid metabolic process / leukotriene-A4 hydrolase activity / soluble epoxide hydrolase / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases ...Synthesis of Leukotrienes (LT) and Eoxins (EX) / Biosynthesis of protectins / Biosynthesis of D-series resolvins / Biosynthesis of E-series 18(S)-resolvins / Biosynthesis of aspirin-triggered D-series resolvins / Biosynthesis of E-series 18(R)-resolvins / cellular lipid metabolic process / leukotriene-A4 hydrolase activity / soluble epoxide hydrolase / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / epoxide hydrolase activity / peptide catabolic process / metalloaminopeptidase activity / aminopeptidase activity / Neutrophil degranulation / protein catabolic process / proteolysis / zinc ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Peptidase M1, leukotriene A4 hydrolase/aminopeptidase C-terminal domain / Leukotriene A4 hydrolase/leucine aminopeptidase / Peptidase M1, leukotriene A4 hydrolase/aminopeptidase C-terminal / Aminopeptidase, leukotriene A4 hydrolase-like / Peptidase M1, LTA-4 hydrolase/aminopeptidase, C-terminal domain superfamily / Leukotriene A4 hydrolase, C-terminal / Leukotriene A4 hydrolase, C-terminal / Zincin-like - #30 / Zincin-like / tricorn interacting facor f3 domain ...Peptidase M1, leukotriene A4 hydrolase/aminopeptidase C-terminal domain / Leukotriene A4 hydrolase/leucine aminopeptidase / Peptidase M1, leukotriene A4 hydrolase/aminopeptidase C-terminal / Aminopeptidase, leukotriene A4 hydrolase-like / Peptidase M1, LTA-4 hydrolase/aminopeptidase, C-terminal domain superfamily / Leukotriene A4 hydrolase, C-terminal / Leukotriene A4 hydrolase, C-terminal / Zincin-like - #30 / Zincin-like / tricorn interacting facor f3 domain / Aminopeptidase N-like , N-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Neutral zinc metallopeptidases, zinc-binding region signature. / Alpha Horseshoe / Armadillo-type fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / Leucine aminopeptidase 2
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsHelgstrand, C. / Hasan, M. / Usyal, H. / Haeggstrom, J.Z. / Thunnissen, M.M.G.M.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: A Leukotriene A(4) Hydrolase-Related Aminopeptidase from Yeast Undergoes Induced Fit Upon Inhibitor Binding.
Authors: Helgstrand, C. / Hasan, M. / Uysal, H. / Haeggstr, J.Z. / Thunnissen, M.M.G.M.
History
DepositionAug 31, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Non-polymer description / Source and taxonomy
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.4Dec 20, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LEUKOTRIENE A-4 HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3614
Polymers72,8961
Non-polymers4653
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)159.556, 159.556, 76.832
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-612-

GLN

21A-2038-

HOH

31A-2084-

HOH

-
Components

#1: Protein LEUKOTRIENE A-4 HYDROLASE / LTA-4 HYDROLASE


Mass: 72896.055 Da / Num. of mol.: 1 / Fragment: RESIDUES 40-671
Source method: isolated from a genetically manipulated source
Details: GLUTATHIONE ATTACHED AT CYS147
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PETM-11, PETM-30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q10740, leukotriene-A4 hydrolase
#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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsGLUTATHIONE (GSH): ATTACHED TO CYS147

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 37 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop
Details: TO OBTAIN DIFFRACTION QUALITY CRYSTALS, HANGING DROPS OF 2 UL OF PROTEIN (6 MG/ML) AND 1 UL OF MOTHER LIQUOR (0.1 M MMT BUFFER, PH 8, 12-14% PEG 6000) WERE ALLOWED TO EQUILIBRATE AGAINST THE ...Details: TO OBTAIN DIFFRACTION QUALITY CRYSTALS, HANGING DROPS OF 2 UL OF PROTEIN (6 MG/ML) AND 1 UL OF MOTHER LIQUOR (0.1 M MMT BUFFER, PH 8, 12-14% PEG 6000) WERE ALLOWED TO EQUILIBRATE AGAINST THE MOTHER LIQUOR FOR 18-24 HOURS BEFORE THE DROPS WERE STREAK SEEDED FROM EARLIER CRYSTALS.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04
DetectorType: MARRESEARCH / Detector: CCD / Details: MULTILAYER MIRROR, CURVED TO FOCUS IN THE VERTICAL
RadiationMonochromator: BENT SI (111) CRYSTAL, HORIZONTALLY FOCUSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 2.7→26 Å / Num. obs: 30000 / % possible obs: 95.3 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 43.62 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.4
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.6 / % possible all: 68.8

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HS6

1hs6


Resolution: 2.73→26.005 Å / SU ML: 0.42 / σ(F): 0.01 / Phase error: 22.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2402 1432 5 %
Rwork0.1747 --
obs0.1779 28409 93.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.816 Å2 / ksol: 0.342 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.949 Å20 Å20 Å2
2--4.949 Å20 Å2
3----9.898 Å2
Refinement stepCycle: LAST / Resolution: 2.73→26.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5122 0 27 114 5263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085287
X-RAY DIFFRACTIONf_angle_d1.1487164
X-RAY DIFFRACTIONf_dihedral_angle_d16.6751912
X-RAY DIFFRACTIONf_chiral_restr0.08770
X-RAY DIFFRACTIONf_plane_restr0.004924
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7262-2.82350.34041180.24252167X-RAY DIFFRACTION77
2.8235-2.93640.30351470.22392430X-RAY DIFFRACTION85
2.9364-3.06990.32131450.21762549X-RAY DIFFRACTION90
3.0699-3.23150.25541200.20412654X-RAY DIFFRACTION93
3.2315-3.43350.25161450.18962798X-RAY DIFFRACTION98
3.4335-3.69790.2911530.16932869X-RAY DIFFRACTION100
3.6979-4.06880.19671550.13722821X-RAY DIFFRACTION99
4.0688-4.65460.15291530.11582834X-RAY DIFFRACTION99
4.6546-5.85330.19351500.12292902X-RAY DIFFRACTION99
5.8533-26.0060.20991460.15592953X-RAY DIFFRACTION99
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)
10.4065-0.4633-0.440.70260.58460.93710.24390.2675-0.1036-0.041-0.11090.1508-0.0638-0.2876-0.0139-0.05840.0005-0.03690.1309-0.10460.0371-13.852773.9873-12.5557
21.0706-0.5749-0.75860.35910.54280.9031-0.33080.2121-0.7478-0.0239-0.21540.41880.0064-0.0650.54430.2545-0.09580.0090.3023-0.07870.575-17.763553.4965-9.5815
30.5514-0.3571-0.55130.37650.18790.71590.0014-0.148-0.00050.0315-0.00880.11920.09170.23280.01050.01950.0138-0.00150.08070.00110.04977.359566.2696-2.8138
40.0743-0.03440.16610.0527-0.12980.45630.0208-0.00620.0065-0.0676-0.06140.00290.17590.26140.04130.14490.17170.00350.22390.0020.047134.555954.6405-13.1015
50.93210.0349-0.08940.0013-0.00330.00850.11960.29840.1395-0.1403-0.1683-0.03580.80280.02720.051.208-0.2110.13190.8279-0.01130.581241.208167.5331-19.12
60.3802-0.30990.16670.3208-0.14160.07490.21720.287-0.0545-0.2163-0.26180.04220.11840.14660.01710.13520.2437-0.05130.185-0.06640.013820.277555.87-28.6895
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 40:221)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 222:238)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 239:503)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 504:562)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 563:569)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 570:671)

+
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://pdbjlvh1.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