[English] 日本語
Yorodumi
- PDB-1djg: PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C-DELTA1 FROM RAT COMPLEX... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1djg
TitlePHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C-DELTA1 FROM RAT COMPLEXED WITH LANTHANUM
ComponentsPHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C, ISOZYME DELTA1
KeywordsLIPID DEGRADATION / PHOSPHORIC DIESTER HYDROLASE / HYDROLASE / TRANSDUCER / CALCIUM-BINDING / PHOSPHOLIPASE C / PHOSPHOINOSITIDE-SPECIFIC
Function / homology
Function and homology information


phospholipase C/protein kinase C signal transduction / positive regulation of inositol trisphosphate biosynthetic process / Synthesis of IP3 and IP4 in the cytosol / response to prostaglandin F / phosphoinositide phospholipase C / response to aluminum ion / positive regulation of norepinephrine secretion / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / phosphatidylinositol metabolic process / phosphatidylinositol-4,5-bisphosphate phospholipase C activity ...phospholipase C/protein kinase C signal transduction / positive regulation of inositol trisphosphate biosynthetic process / Synthesis of IP3 and IP4 in the cytosol / response to prostaglandin F / phosphoinositide phospholipase C / response to aluminum ion / positive regulation of norepinephrine secretion / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / phosphatidylinositol metabolic process / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / inositol 1,4,5 trisphosphate binding / calcium-dependent phospholipid binding / GTPase activating protein binding / labyrinthine layer blood vessel development / response to hyperoxia / lipid catabolic process / phosphatidylinositol-4,5-bisphosphate binding / cellular response to calcium ion / response to peptide hormone / response to calcium ion / mitochondrial membrane / phospholipid binding / regulation of cell population proliferation / angiogenesis / phospholipase C-activating G protein-coupled receptor signaling pathway / G protein-coupled receptor signaling pathway / calcium ion binding / enzyme binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-1 / : / Phosphoinositide-specific phospholipase C, EF-hand-like domain / Phosphoinositide-specific phospholipase C, efhand-like / Pleckstrin homology domain / Phosphatidylinositol (PI) phosphodiesterase / Phosphoinositide phospholipase C family / Phospholipase C, phosphatidylinositol-specific, Y domain / Phosphatidylinositol-specific phospholipase C, Y domain / Phosphatidylinositol-specific phospholipase Y-box domain profile. ...1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-1 / : / Phosphoinositide-specific phospholipase C, EF-hand-like domain / Phosphoinositide-specific phospholipase C, efhand-like / Pleckstrin homology domain / Phosphatidylinositol (PI) phosphodiesterase / Phosphoinositide phospholipase C family / Phospholipase C, phosphatidylinositol-specific, Y domain / Phosphatidylinositol-specific phospholipase C, Y domain / Phosphatidylinositol-specific phospholipase Y-box domain profile. / Phospholipase C, catalytic domain (part); domain Y / Phosphatidylinositol-specific phospholipase C, X domain / Phosphatidylinositol-specific phospholipase C, X domain / Phospholipase C, catalytic domain (part); domain X / Phosphatidylinositol-specific phospholipase X-box domain profile. / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / EF-hand / Recoverin; domain 1 / C2 domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / PH-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / LANTHANUM (III) ION / 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsEssen, L.-O. / Perisic, O. / Williams, R.L.
CitationJournal: Biochemistry / Year: 1997
Title: A ternary metal binding site in the C2 domain of phosphoinositide-specific phospholipase C-delta1.
Authors: Essen, L.O. / Perisic, O. / Lynch, D.E. / Katan, M. / Williams, R.L.
History
DepositionSep 25, 1996Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 27, 2018Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_conn_angle ...pdbx_database_status / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn
Item: _pdbx_database_status.process_site
Revision 1.4Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C, ISOZYME DELTA1
B: PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C, ISOZYME DELTA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,37812
Polymers141,1492
Non-polymers1,22910
Water12,755708
1
A: PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C, ISOZYME DELTA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1896
Polymers70,5751
Non-polymers6155
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C, ISOZYME DELTA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1896
Polymers70,5751
Non-polymers6155
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)397.920, 397.920, 397.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number210
Space group name H-MF4132
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.657608, -0.009698, 0.753298), (0.098559, 0.992431, -0.073262), (-0.746886, 0.122422, 0.653586)90.078, -10.519, 90.31
2given(0.646684, -0.041248, 0.761642), (0.092036, 0.995461, -0.024235), (-0.757185, 0.085771, 0.647545)91.7698, -8.2721, 91.109
3given(0.650942, -0.026581, 0.758662), (0.076892, 0.996556, -0.031058), (-0.755223, 0.078552, 0.650744)90.8218, -7.2061, 91.345

-
Components

#1: Protein PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C, ISOZYME DELTA1 / PLC-D1


Mass: 70574.516 Da / Num. of mol.: 2 / Mutation: DEL(1-132) DELETION VARIANT
Source method: isolated from a genetically manipulated source
Details: CATALYTICALLY-ACTIVE DELETION VARIANT THAT LACKS AN N-TERMINAL PH DOMAIN, COMPLEXED WITH LANTHANUM
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: CDNA FRAGMENT / Plasmid: PGEX (PHARMACIA) / Gene (production host): CDNA FRAGMENT / Production host: Escherichia coli (E. coli)
References: UniProt: P10688, phosphoinositide phospholipase C
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-LA / LANTHANUM (III) ION


Mass: 138.905 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: La
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 708 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 4.65 Å3/Da / Density % sol: 70 %
Crystal grow
*PLUS
Temperature: 12 ℃ / pH: 8 / Method: vapor diffusion, hanging drop / Details: Essen, L.O., (1996) Nature, 380, 595.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.4 Mammonium phosphate1reservoir
25 mg/mlprotein1drop
35 mMTris-HCl1drop
450 mM1dropNaCl
50.25 mMEGTA1drop
60.5 mMDTT1drop
70.005 %(w/v)sodium azide1drop
80.05 %(w/v)CHAPSO1drop
90.7 Mammonium phosphate1drop

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.89
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 4, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89 Å / Relative weight: 1
ReflectionNum. obs: 81095 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.042
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 53 Å / Num. measured all: 384052
Reflection shell
*PLUS
% possible obs: 90.2 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.17

-
Processing

Software
NameVersionClassification
TNT5Erefinement
MOSFLMdata reduction
RefinementResolution: 2.6→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.27 3297 4 %
Rwork0.21 --
all-77696 -
obs-77696 98.5 %
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8522 0 16 708 9246
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01687231
X-RAY DIFFRACTIONt_angle_deg1.41117501.2
X-RAY DIFFRACTIONt_dihedral_angle_d18.2851860
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0162291
X-RAY DIFFRACTIONt_gen_planes0.0162291
X-RAY DIFFRACTIONt_it2.6465
X-RAY DIFFRACTIONt_nbd0.06330120
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_planar_d0.0161
X-RAY DIFFRACTIONt_plane_restr0.0161

+
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