[English] 日本語
Yorodumi
- PDB-7zot: crystal structure of PLAAT4 N-terminal domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zot
Titlecrystal structure of PLAAT4 N-terminal domain
ComponentsPhospholipase A and acyltransferase 4
KeywordsHYDROLASE / phospholipase A1/A2 / acyltransferase / catalytic domain / soluble domain / cytosolic protein
Function / homology
Function and homology information


positive regulation of protein-glutamine gamma-glutamyltransferase activity / phosphatidylethanolamine acyl-chain remodeling / N-acylphosphatidylethanolamine metabolic process / phospholipase A1 / phosphatidylserine 1-acylhydrolase activity / 1-acyl-2-lysophosphatidylserine acylhydrolase activity / phospholipase A1 activity / Acyl chain remodelling of PE / N-acyltransferase activity / phospholipase A2 activity ...positive regulation of protein-glutamine gamma-glutamyltransferase activity / phosphatidylethanolamine acyl-chain remodeling / N-acylphosphatidylethanolamine metabolic process / phospholipase A1 / phosphatidylserine 1-acylhydrolase activity / 1-acyl-2-lysophosphatidylserine acylhydrolase activity / phospholipase A1 activity / Acyl chain remodelling of PE / N-acyltransferase activity / phospholipase A2 activity / positive regulation of keratinocyte differentiation / phospholipase A2 / acyltransferase activity / phospholipid metabolic process / lipid catabolic process / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / negative regulation of cell population proliferation / membrane / cytoplasm / cytosol
Similarity search - Function
Lecithin retinol acyltransferase / LRAT domain profile. / LRAT domain
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Phospholipase A and acyltransferase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.735 Å
Authorsvon Castelmur, E. / Perrakis, A. / Cornaciu, I.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: J.Struct.Biol. / Year: 2022
Title: Crystal structure of the phospholipase A and acyltransferase 4 (PLAAT4) catalytic domain.
Authors: Wehlin, A. / Cornaciu, I. / Marquez, J.A. / Perrakis, A. / von Castelmur, E.
History
DepositionApr 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phospholipase A and acyltransferase 4
B: Phospholipase A and acyltransferase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1983
Polymers28,0922
Non-polymers1061
Water1,76598
1
A: Phospholipase A and acyltransferase 4


Theoretical massNumber of molelcules
Total (without water)14,0461
Polymers14,0461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phospholipase A and acyltransferase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1522
Polymers14,0461
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.800, 39.540, 52.950
Angle α, β, γ (deg.)90.000, 94.952, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Phospholipase A and acyltransferase 4 / HRAS-like suppressor 4 / HRSL4 / RAR-responsive protein TIG3 / Retinoic acid receptor responder ...HRAS-like suppressor 4 / HRSL4 / RAR-responsive protein TIG3 / Retinoic acid receptor responder protein 3 / Retinoid-inducible gene 1 protein / Tazarotene-induced gene 3 protein


Mass: 14045.846 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLAAT4, RARRES3, RIG1, TIG3 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9UL19, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups, phospholipase A1, phospholipase A2
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpheus screen condition H12 0.1M Amino acids, 0.1M Tris Bicine pH 8.5 37.5% v/v MPD PEG1000 PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.735→52.752 Å / Num. obs: 23862 / % possible obs: 94.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 20.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.036 / Rrim(I) all: 0.066 / Net I/σ(I): 13.8
Reflection shellResolution: 1.735→1.765 Å / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1079 / CC1/2: 0.781 / Rpim(I) all: 0.322 / Rrim(I) all: 0.58

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ZOM

7zom


Resolution: 1.735→52.752 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.948 / Cross valid method: FREE R-VALUE / ESU R: 0.123 / ESU R Free: 0.108
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2009 1151 4.824 %
Rwork0.184 22710 -
all0.185 --
obs-23861 94.518 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 21.369 Å2
Baniso -1Baniso -2Baniso -3
1--0.614 Å2-0 Å20.689 Å2
2--0.585 Å2-0 Å2
3----0.089 Å2
Refinement stepCycle: LAST / Resolution: 1.735→52.752 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1872 0 7 98 1977
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0121990
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.6372710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6745257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.45221.351111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.2815338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8711516
X-RAY DIFFRACTIONr_chiral_restr0.070.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021562
X-RAY DIFFRACTIONr_nbd_refined0.2030.2819
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21336
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2105
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1480.276
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1340.216
X-RAY DIFFRACTIONr_mcbond_it3.141.728966
X-RAY DIFFRACTIONr_mcangle_it4.2482.5711210
X-RAY DIFFRACTIONr_scbond_it5.1822.2591024
X-RAY DIFFRACTIONr_scangle_it7.373.1811488
X-RAY DIFFRACTIONr_lrange_it8.63924.9532933
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.735-1.780.264780.2621519X-RAY DIFFRACTION87.5548
1.78-1.8280.356770.261589X-RAY DIFFRACTION91.6392
1.828-1.8810.282760.2281613X-RAY DIFFRACTION94.8344
1.881-1.9390.268570.2121272X-RAY DIFFRACTION79.0131
1.939-2.0030.17760.1911559X-RAY DIFFRACTION98.494
2.003-2.0730.208720.1851308X-RAY DIFFRACTION85.7143
2.073-2.1510.187630.171391X-RAY DIFFRACTION96.6755
2.151-2.2390.206630.1731419X-RAY DIFFRACTION98.8659
2.239-2.3380.186730.1761350X-RAY DIFFRACTION98.6824
2.338-2.4520.221610.1781298X-RAY DIFFRACTION98.6928
2.452-2.5840.153570.181214X-RAY DIFFRACTION98.8336
2.584-2.7410.212740.1771139X-RAY DIFFRACTION98.5378
2.741-2.930.228520.1851097X-RAY DIFFRACTION98.7113
2.93-3.1640.242560.183999X-RAY DIFFRACTION97.235
3.164-3.4650.205470.177943X-RAY DIFFRACTION98.2143
3.465-3.8720.142470.154846X-RAY DIFFRACTION97.3828
3.872-4.4670.173390.15739X-RAY DIFFRACTION96.4064
4.467-5.4630.178340.182626X-RAY DIFFRACTION97.0588
5.463-7.6930.212330.235501X-RAY DIFFRACTION96.7391
7.693-52.7520.235160.217288X-RAY DIFFRACTION95.899

+
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