[English] 日本語
Yorodumi
- PDB-6kz8: Crystal structure of plant Phospholipase D alpha complex with pho... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kz8
TitleCrystal structure of plant Phospholipase D alpha complex with phosphatidic acid
ComponentsPhospholipase D alpha 1
KeywordsHYDROLASE / Phospholipase D / calcium activation / C2 domain / phosphatidic acid / inhibitor
Function / homology
Function and homology information


leaf shaping / positive regulation of abscisic acid-activated signaling pathway / phospholipase activity / seed germination / ethylene-activated signaling pathway / regulation of stomatal movement / phospholipase D / phosphatidylcholine metabolic process / phospholipase D activity / response to abscisic acid ...leaf shaping / positive regulation of abscisic acid-activated signaling pathway / phospholipase activity / seed germination / ethylene-activated signaling pathway / regulation of stomatal movement / phospholipase D / phosphatidylcholine metabolic process / phospholipase D activity / response to abscisic acid / plasmodesma / abscisic acid-activated signaling pathway / vacuole / clathrin-coated vesicle / lipid catabolic process / phosphatidylinositol-4,5-bisphosphate binding / GTPase activator activity / chloroplast / fatty acid metabolic process / mitochondrial membrane / calcium ion binding / endoplasmic reticulum / mitochondrion / membrane / nucleus / plasma membrane / cytosol
Similarity search - Function
Phospholipase D, plant / Phospholipase D, C-terminal / Phospholipase D C terminal / Phospholipase D family / Phospholipase D Active site motif / Phospholipase D. Active site motifs. / Phospholipase D/Transphosphatidylase / Phospholipase D phosphodiesterase active site profile. / Protein kinase C conserved region 2 (CalB) / C2 domain ...Phospholipase D, plant / Phospholipase D, C-terminal / Phospholipase D C terminal / Phospholipase D family / Phospholipase D Active site motif / Phospholipase D. Active site motifs. / Phospholipase D/Transphosphatidylase / Phospholipase D phosphodiesterase active site profile. / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily
Similarity search - Domain/homology
1,2-DIOCTANOYL-SN-GLYCERO-3-PHOSPHATE / Phospholipase D alpha 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.291 Å
AuthorsLi, J.X. / Yu, F. / Zhang, P.
Funding support China, 6items
OrganizationGrant numberCountry
National Natural Science Foundation of China2018YFA0900600 China
National Natural Science Foundation of China31971120 China
National Natural Science Foundation of China31870720 China
Chinese Academy of SciencesXDB27020103 China
Chinese Academy of SciencesQYZDB-SSW-SMC006 China
National Natural Science Foundation of China19XD1424500 China
CitationJournal: Cell Res. / Year: 2020
Title: Crystal structure of plant PLD alpha 1 reveals catalytic and regulatory mechanisms of eukaryotic phospholipase D.
Authors: Li, J. / Yu, F. / Guo, H. / Xiong, R. / Zhang, W. / He, F. / Zhang, M. / Zhang, P.
History
DepositionSep 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 13, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phospholipase D alpha 1
B: Phospholipase D alpha 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,8636
Polymers183,9362
Non-polymers9274
Water8,953497
1
A: Phospholipase D alpha 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,4323
Polymers91,9681
Non-polymers4642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint5 kcal/mol
Surface area30160 Å2
MethodPISA
2
B: Phospholipase D alpha 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,4323
Polymers91,9681
Non-polymers4642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint5 kcal/mol
Surface area29660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.042, 123.030, 138.904
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Phospholipase D alpha 1 / Phospholipase D / PLD alpha 1 / Choline phosphatase 1 / PLDalpha / Phosphatidylcholine-hydrolyzing ...Phospholipase D / PLD alpha 1 / Choline phosphatase 1 / PLDalpha / Phosphatidylcholine-hydrolyzing phospholipase D 1


Mass: 91967.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PLDALPHA1, PLD1, At3g15730, MSJ11.13 / Production host: Escherichia coli (E. coli) / References: UniProt: Q38882, phospholipase D
#2: Chemical ChemComp-PA8 / 1,2-DIOCTANOYL-SN-GLYCERO-3-PHOSPHATE


Mass: 423.458 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H36O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG 3000, 0.1M Tris-HCl (pH 7.0), 0.2M Ca(OAc)2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9798 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.29→37.89 Å / Num. obs: 101062 / % possible obs: 99.8 % / Redundancy: 12.6 % / CC1/2: 0.992 / Net I/σ(I): 27.6
Reflection shellResolution: 2.3→2.37 Å / Num. unique obs: 6209 / CC1/2: 0.785

-
Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.291→37.89 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2446 2720 2.69 %
Rwork0.1979 98342 -
obs0.1992 101062 68.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.69 Å2 / Biso mean: 15.7814 Å2 / Biso min: 1.2 Å2
Refinement stepCycle: final / Resolution: 2.291→37.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12596 0 58 497 13151
Biso mean--15.17 14.75 -
Num. residues----1568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01312978
X-RAY DIFFRACTIONf_angle_d1.617584
X-RAY DIFFRACTIONf_chiral_restr0.2111854
X-RAY DIFFRACTIONf_plane_restr0.012302
X-RAY DIFFRACTIONf_dihedral_angle_d21.6324828
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.291-2.33260.3344820.2695294139
2.3326-2.37750.3101920.2608337745
2.3775-2.4260.3422980.2691354447
2.426-2.47880.32311020.2715366848
2.4788-2.53640.28041020.2722375250
2.5364-2.59980.31090.2807384251
2.5998-2.67010.2961090.2727396452
2.6701-2.74870.32331140.263408754
2.7487-2.83730.28811160.2449433657
2.8373-2.93870.25531290.2391458161
2.9387-3.05630.26951340.2327502867
3.0563-3.19540.23471590.2156556773
3.1954-3.36370.27761750.2005628084
3.3637-3.57430.22381850.1823675890
3.5743-3.85010.24281930.1691708794
3.8501-4.2370.23192030.1645716795
4.237-4.84910.18812100.1598743999
4.8491-6.10520.22282080.18117516100
6.1052-37.890.2372000.1883740898

+
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