[English] 日本語
Yorodumi
- PDB-1beo: BETA-CRYPTOGEIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1beo
TitleBETA-CRYPTOGEIN
ComponentsBETA-CRYPTOGEIN
KeywordsFUNGAL TOXIC ELICITOR / ELICITIN / TOXIN / PLANT PATHOGEN
Function / homology
Function and homology information


symbiont-mediated perturbation of host defense-related programmed cell death / symbiont-mediated killing of host cell / extracellular region
Similarity search - Function
Beta-cryptogein / Elicitin domain / Elicitin / Elicitin superfamily / Elicitin / Elicitin / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Beta-elicitin cryptogein
Similarity search - Component
Biological speciesPhytophthora cryptogea (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, NATIVE DATA / Resolution: 2.2 Å
AuthorsBoissy, G. / De La Fortelle, E. / Kahn, R. / Huet, J.C. / Bricogne, G. / Pernollet, J.C. / Brunie, S.
Citation
Journal: Structure / Year: 1996
Title: Crystal structure of a fungal elicitor secreted by Phytophthora cryptogea, a member of a novel class of plant necrotic proteins.
Authors: Boissy, G. / de La Fortelle, E. / Kahn, R. / Huet, J.C. / Bricogne, G. / Pernollet, J.C. / Brunie, S.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization and Preliminary X-Ray Diffraction Studies of Beta-Cryptogein, a Toxic Elicitin Secreted by the Phytopathogenic Fungus Phytophthora Cryptogea
Authors: Guilloteau, J.P. / Nespoulous, C. / Huet, J.C. / Beauvais, F. / Pernollet, J.C. / Brunie, S.
History
DepositionAug 2, 1996Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BETA-CRYPTOGEIN


Theoretical massNumber of molelcules
Total (without water)10,3411
Polymers10,3411
Non-polymers00
Water1,18966
1
A: BETA-CRYPTOGEIN

A: BETA-CRYPTOGEIN


Theoretical massNumber of molelcules
Total (without water)20,6822
Polymers20,6822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-1/41
Unit cell
Length a, b, c (Å)46.510, 46.510, 134.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

-
Components

#1: Protein BETA-CRYPTOGEIN / BETA-ELICITIN OF PHYTOPHTHORA CRYPTOGEA


Mass: 10340.815 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Phytophthora cryptogea (eukaryote) / References: UniProt: P15570
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.7 Å3/Da / Density % sol: 66 %
Description: PHASING: 4 WAVELENGTHS MAD DATA COLLECTION IN THE VICINITY OF THE PLATINUM LIII ABSORPTION EDGE (ESRF D2AM, 26-08-95).
Crystal growpH: 7.5 / Details: 4.85 M NACL, PH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: used to seeding / PH range low: 10 / PH range high: 4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
175 mg/mlprotein1drop
20.02 %1dropNaN3
310 mM1dropNaCl
44.85 M1reservoirNaCl
550 mMsodium acetate1reservoir
650 mMTris-HCl1reservoircan be replaced by 50mM CAPS

-
Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 22, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionNum. obs: 7864 / % possible obs: 97.2 % / Observed criterion σ(I): 3 / Redundancy: 3.1 % / Biso Wilson estimate: 38 Å2 / Rsym value: 0.032
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. measured all: 35101 / Rmerge(I) obs: 0.032
Reflection shell
*PLUS
Rmerge(I) obs: 0.15

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SHARPphasing
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MAD, NATIVE DATA / Resolution: 2.2→7 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.279 -7.5 %
Rwork0.218 --
obs0.218 6987 -
Displacement parametersBiso mean: 37.3 Å2
Refinement stepCycle: LAST / Resolution: 2.2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms717 0 0 66 783
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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 / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Num. reflection all: 7583 / Num. reflection Rfree: 596
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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