[English] 日本語
Yorodumi
- PDB-6v4m: Trichuris suis BCL-2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6v4m
TitleTrichuris suis BCL-2
ComponentsBCL-2
KeywordsAPOPTOSIS / BCL-2 / helical bundle
Function / homology
Function and homology information


regulation of apoptotic process / membrane => GO:0016020 / apoptotic process
Similarity search - Function
Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl2-like / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesTrichuris suis (pig whipworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.599 Å
AuthorsFairlie, W.D. / Lee, E.F. / Smith, B.J.
CitationJournal: Commun Biol / Year: 2020
Title: Diversity in the intrinsic apoptosis pathway of nematodes.
Authors: Young, N.D. / Harris, T.J. / Evangelista, M. / Tran, S. / Wouters, M.A. / Soares da Costa, T.P. / Kershaw, N.J. / Gasser, R.B. / Smith, B.J. / Lee, E.F. / Fairlie, W.D.
History
DepositionNov 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BCL-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7755
Polymers19,5721
Non-polymers2024
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.248, 55.248, 111.249
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-425-

HOH

-
Components

#1: Protein BCL-2


Mass: 19572.486 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichuris suis (pig whipworm) / Gene: M513_07322, M514_07322 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A085NFU1
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 43.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-chloride pH8.5, 0.2M Lithium sulphate, 2M sodium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.599→39.199 Å / Num. obs: 23576 / % possible obs: 99.9 % / Redundancy: 14.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Net I/σ(I): 25.15
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 3.94 / Num. unique obs: 3723 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.11_2567refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Auto-Rickshawphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FDL Chain A

3fdl


Resolution: 1.599→39.199 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.46
RfactorNum. reflection% reflection
Rfree0.1916 1179 5 %
Rwork0.1689 --
obs0.17 23576 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.44 Å2 / Biso mean: 21.1672 Å2 / Biso min: 8.87 Å2
Refinement stepCycle: final / Resolution: 1.599→39.199 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1279 0 8 121 1408
Biso mean--71.33 30.52 -
Num. residues----163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061361
X-RAY DIFFRACTIONf_angle_d0.7741851
X-RAY DIFFRACTIONf_chiral_restr0.046204
X-RAY DIFFRACTIONf_plane_restr0.005232
X-RAY DIFFRACTIONf_dihedral_angle_d12.659814
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.599-1.67150.24531440.21652733
1.6715-1.75960.18851440.18562736
1.7596-1.86980.18231450.17582756
1.8698-2.01420.21671450.17212752
2.0142-2.21690.18861460.16232783
2.2169-2.53760.21071470.16382789
2.5376-3.19690.19721490.18452839
3.1969-3.91990.16971590.15413009
Refinement TLS params.Method: refined / Origin x: 36.4645 Å / Origin y: -5.4155 Å / Origin z: 38.9164 Å
111213212223313233
T0.0801 Å2-0.006 Å2-0.0017 Å2-0.1179 Å20.0018 Å2--0.1027 Å2
L1.1453 °20.0845 °20.4285 °2-1.1668 °20.2686 °2--1.7896 °2
S-0.022 Å °0.084 Å °-0.055 Å °-0.0089 Å °0.0123 Å °-0.0118 Å °-0.0038 Å °0.098 Å °0.011 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA6 - 168
2X-RAY DIFFRACTION1allZ2 - 156
3X-RAY DIFFRACTION1allC1 - 3
4X-RAY DIFFRACTION1allB1

+
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