[English] 日本語
Yorodumi
- PDB-1gym: PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C IN COMPLEX WITH GLU... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gym
TitlePHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C IN COMPLEX WITH GLUCOSAMINE-(ALPHA-1-6)-MYO-INOSITOL
ComponentsPHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C
KeywordsHYDROLASE (PHOSPHORIC DIESTER) / PHOSPHATIDYLINOSITOL SPECIFIC PHOSPHOLIPASE C / GLUCOSAMINYL (ALPHA-1-6)-D-MYO-INOSITOL / INHIBITOR COMPLEX / LIPID DEGRADATION
Function / homology
Function and homology information


phosphatidylinositol diacylglycerol-lyase / phosphatidylinositol diacylglycerol-lyase activity / phosphoric diester hydrolase activity / lipid catabolic process / extracellular region
Similarity search - Function
: / Phosphatidylinositol (PI) phosphodiesterase / 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 / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-MYG / 1-phosphatidylinositol phosphodiesterase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsHeinz, D.W. / Ryan, M. / Smith, M.P. / Weaver, L.H. / Keana, J.F.W. / Griffith, O.H.
Citation
Journal: Biochemistry / Year: 1996
Title: Crystal structure of phosphatidylinositol-specific phospholipase C from Bacillus cereus in complex with glucosaminyl(alpha 1-->6)-D-myo-inositol, an essential fragment of GPI anchors.
Authors: Heinz, D.W. / Ryan, M. / Smith, M.P. / Weaver, L.H. / Keana, J.F. / Griffith, O.H.
#1: Journal: Embo J. / Year: 1995
Title: Crystal Structure of the Phosphatidylinositol-Specific Phospholipase C from Bacillus Cereus in Complex with Myo-Inositol
Authors: Heinz, D.W. / Ryan, M. / Bullock, T.L. / Griffith, O.H.
#2: Journal: Biophys.J. / Year: 1993
Title: Crystallization of Phosphatidylinositol-Specific Phospholipase C from Bacillus Cereus
Authors: Bullock, T.L. / Ryan, M. / Kim, S.L. / Remington, S.J. / Griffith, O.H.
#3: Journal: J.Bacteriol. / Year: 1989
Title: Phosphatidylinositol-Specific Phospholipase C of Bacillus Cereus: Cloning, Sequencing, and Relationship to Other Phospholipases
Authors: Kuppe, A. / Evans, L.M. / Mcmillen, D.A. / Griffith, O.H.
History
DepositionMay 2, 1996Processing site: BNL
Revision 1.0Nov 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 7, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9102
Polymers34,5691
Non-polymers3411
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.200, 46.500, 161.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C


Mass: 34568.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: PI-PLC GENE / Plasmid: PBR322 RELATED / Gene (production host): PI-PLC GENE / Production host: Escherichia coli (E. coli) / References: UniProt: P14262, EC: 3.1.4.10
#2: Sugar ChemComp-MYG / (1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl 2-amino-2-deoxy-alpha-D-glucopyranoside / GLUCOSAMINYL-(ALPHA-6)-D-MYO-INOSITOL / (1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl 2-amino-2-deoxy-alpha-D-glucoside / (1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl 2-amino-2-deoxy-D-glucoside / (1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl 2-amino-2-deoxy-glucoside


Type: D-saccharide / Mass: 341.312 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H23NO10
IdentifierTypeProgram
glucosaminyl-(alpha-6)-D-myo-inositolIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 45 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14 mg/mlPI-PLC1drop
215 mMGlcN(alpha1-6)Ins.1drop
320 mMHEPES1drop
40.005 %1dropNaN3
518.5 %PEG6001drop
60.095 Mtrisodium citrate1drop
71.25 mMbeta-mercaptoethanol1drop
82.25 M1reservoirNaCl

-
Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Jul 22, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 15359 / % possible obs: 72.4 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.043
Reflection
*PLUS
% possible obs: 75 % / Num. measured all: 32130 / Rmerge(I) obs: 0.047
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.22 Å / % possible obs: 62.2 % / Mean I/σ(I) obs: 3.1

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DETECTORSUPPLIED SOFTWAREdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.2→8 Å / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.272 -10 %
Rwork0.178 --
obs0.178 14670 75 %
Displacement parametersBiso mean: 20.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2991 0 0 137 3128
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.8
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.8

+
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