[English] 日本語
Yorodumi
- PDB-4j7y: Human LTC4 synthase in complex with product analogs - implication... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4j7y
TitleHuman LTC4 synthase in complex with product analogs - implications for enzyme catalysis
ComponentsLeukotriene C4 synthase
KeywordsLYASE / Leukotriene C4 synthase / product analogs / lipid biosynthesis
Function / homology
Function and homology information


Biosynthesis of protectin and resolvin conjugates in tissue regeneration (PCTR and RCTR) / Biosynthesis of maresin conjugates in tissue regeneration (MCTR) / leukotriene-C4 synthase / leukotriene-C4 synthase activity / Biosynthesis of Lipoxins (LX) / Synthesis of 5-eicosatetraenoic acids / leukotriene metabolic process / Transferases; Transferring alkyl or aryl groups, other than methyl groups / Synthesis of Leukotrienes (LT) and Eoxins (EX) / leukotriene biosynthetic process ...Biosynthesis of protectin and resolvin conjugates in tissue regeneration (PCTR and RCTR) / Biosynthesis of maresin conjugates in tissue regeneration (MCTR) / leukotriene-C4 synthase / leukotriene-C4 synthase activity / Biosynthesis of Lipoxins (LX) / Synthesis of 5-eicosatetraenoic acids / leukotriene metabolic process / Transferases; Transferring alkyl or aryl groups, other than methyl groups / Synthesis of Leukotrienes (LT) and Eoxins (EX) / leukotriene biosynthetic process / glutathione peroxidase activity / nuclear outer membrane / long-chain fatty acid biosynthetic process / glutathione transferase activity / enzyme activator activity / nuclear envelope / nuclear membrane / intracellular membrane-bounded organelle / lipid binding / endoplasmic reticulum membrane / endoplasmic reticulum / identical protein binding / membrane
Similarity search - Function
5-lipoxygenase-activating protein / FLAP/GST2/LTC4S, conserved site / : / FLAP/GST2/LTC4S family signature. / Membrane associated eicosanoid/glutathione metabolism-like domain / Membrane-associated, eicosanoid/glutathione metabolism (MAPEG) protein / Membrane associated eicosanoid/glutathione metabolism-like domain superfamily / MAPEG family / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-1JP / NICKEL (II) ION / Leukotriene C4 synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.901 Å
AuthorsNiegowski, D. / Rinaldo-Matthis, A. / Haeggstrom, J.Z.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Crystal Structures of Leukotriene C4 Synthase in Complex with Product Analogs: IMPLICATIONS FOR THE ENZYME MECHANISM.
Authors: Niegowski, D. / Kleinschmidt, T. / Olsson, U. / Ahmad, S. / Rinaldo-Matthis, A. / Haeggstrom, J.Z.
History
DepositionFeb 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references
Revision 1.2Mar 12, 2014Group: Database references
Revision 1.3Sep 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 / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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 C4 synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0204
Polymers17,4121
Non-polymers6083
Water00
1
A: Leukotriene C4 synthase
hetero molecules

A: Leukotriene C4 synthase
hetero molecules

A: Leukotriene C4 synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,05912
Polymers52,2353
Non-polymers1,8259
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation24_544-y,-z-1/2,x-1/21
crystal symmetry operation30_554z+1/2,-x,-y-1/21
Buried area7560 Å2
ΔGint-113 kcal/mol
Surface area20570 Å2
MethodPISA
2
A: Leukotriene C4 synthase
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)216,23848
Polymers208,93912
Non-polymers7,29936
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_554-x,y,-z-11
crystal symmetry operation4_554x,-y,-z-11
crystal symmetry operation21_554y,z+1/2,x-1/21
crystal symmetry operation22_554-y,z+1/2,-x-1/21
crystal symmetry operation23_544y,-z-1/2,-x-1/21
crystal symmetry operation24_544-y,-z-1/2,x-1/21
crystal symmetry operation29_554z+1/2,x,y-1/21
crystal symmetry operation30_554z+1/2,-x,-y-1/21
crystal symmetry operation31_454-z-1/2,-x,y-1/21
crystal symmetry operation32_454-z-1/2,x,-y-1/21
Buried area35840 Å2
ΔGint-497 kcal/mol
Surface area77530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.275, 169.275, 169.275
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23
Components on special symmetry positions
IDModelComponents
11A-201-

NI

21A-202-

SO4

-
Components

#1: Protein Leukotriene C4 synthase / LTC4 synthase / Leukotriene-C(4) synthase


Mass: 17411.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LTC4S / Production host: Pichia Pastoris (fungus) / References: UniProt: Q16873, leukotriene-C4 synthase
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-1JP / D-gamma-glutamyl-(Z)-N-(carboxymethylidene)-S-[(2R)-2-hydroxy-4-phenylbutyl]-L-cysteinamide


Mass: 453.509 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H27N3O7S

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.8 Å3/Da / Density % sol: 78.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.2
Details: 1.8 M NH4SO4, 0.2 M NaCl, 0.1 M Na-cacadylate, pH 6.2, VAPOR DIFFUSION, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93937 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93937 Å / Relative weight: 1
ReflectionResolution: 2.901→32.653 Å / Num. all: 9030 / Num. obs: 9030 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 15.6 % / Rsym value: 0.292 / Net I/σ(I): 7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.9-3.0615.70.0610.16.1341100
3.06-3.2415.90.0610.23.4771100
3.24-3.4715.80.0610.41.9611100
3.47-3.7415.80.0610.90.8811100
3.74-4.115.80.0611.90.3981100
4.1-4.5915.70.06140.1761100
4.59-5.2915.50.0614.40.1581100
5.29-6.4815.50.0613.80.1891100
6.48-9.1714.80.0614.30.121100
9.17-34.553140.06150.108197.3

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.42 Å29.92 Å
Translation6.42 Å29.92 Å

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASER2.5.2phasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2UUI

2uui


Resolution: 2.901→29.924 Å / Occupancy max: 1 / Occupancy min: 0.33 / SU ML: 0.59 / σ(F): 1.33 / Phase error: 33.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2632 439 4.87 %
Rwork0.2495 --
obs0.2502 9020 99.88 %
all-9020 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.4109 Å2
Refinement stepCycle: LAST / Resolution: 2.901→29.924 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1156 0 37 0 1193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061226
X-RAY DIFFRACTIONf_angle_d1.41670
X-RAY DIFFRACTIONf_dihedral_angle_d15.643426
X-RAY DIFFRACTIONf_chiral_restr0.115190
X-RAY DIFFRACTIONf_plane_restr0.006208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9013-3.32070.38681550.34842830X-RAY DIFFRACTION100
3.3207-4.18190.27871280.27892846X-RAY DIFFRACTION100
4.1819-29.92550.2331560.22152905X-RAY DIFFRACTION100

+
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