[English] 日本語
Yorodumi
- PDB-5twa: Crystal structure of Geodia cydonium BHP2 in complex with Lubomir... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5twa
TitleCrystal structure of Geodia cydonium BHP2 in complex with Lubomirskia baicalensis Bak-2
Components
  • BAK-2 protein
  • Bcl-x homologous protein, BHP2
KeywordsAPOPTOSIS / BHP2 / LB-Bak-2 / sponge / Bcl-2
Function / homology
Function and homology information


extrinsic apoptotic signaling pathway in absence of ligand / intrinsic apoptotic signaling pathway in response to DNA damage / regulation of apoptotic process / mitochondrial outer membrane / protein heterodimerization activity / apoptotic process / protein homodimerization activity / membrane
Similarity search - Function
Bcl-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily
Similarity search - Domain/homology
BAK-2 protein / Bcl-x homologous protein, BHP2
Similarity search - Component
Biological speciesGeodia cydonium (invertebrata)
Lubomirskia baicalensis (Lake Baikal sponge)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsCaria, S. / Hinds, M.G. / Kvansakul, M.
CitationJournal: Cell Death Dis / Year: 2017
Title: Structural insight into an evolutionarily ancient programmed cell death regulator - the crystal structure of marine sponge BHP2 bound to LB-Bak-2.
Authors: Caria, S. / Hinds, M.G. / Kvansakul, M.
History
DepositionNov 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bcl-x homologous protein, BHP2
D: BAK-2 protein
B: Bcl-x homologous protein, BHP2
C: BAK-2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,03626
Polymers47,2304
Non-polymers1,80622
Water3,081171
1
A: Bcl-x homologous protein, BHP2
D: BAK-2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,51813
Polymers23,6152
Non-polymers90311
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint7 kcal/mol
Surface area9170 Å2
MethodPISA
2
B: Bcl-x homologous protein, BHP2
C: BAK-2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,51813
Polymers23,6152
Non-polymers90311
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint5 kcal/mol
Surface area9290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.311, 51.594, 107.802
Angle α, β, γ (deg.)90.00, 96.34, 90.00
Int Tables number5
Space group name H-MI121

-
Components

#1: Protein Bcl-x homologous protein, BHP2


Mass: 20864.043 Da / Num. of mol.: 2 / Fragment: UNP residues 19-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geodia cydonium (invertebrata) / Gene: bhp2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q967D2
#2: Protein/peptide BAK-2 protein


Mass: 2750.951 Da / Num. of mol.: 2 / Fragment: UNP residues 64-88 / Source method: obtained synthetically
Source: (synth.) Lubomirskia baicalensis (Lake Baikal sponge)
References: UniProt: Q1RPT5
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2 Å3/Da / Density % sol: 38.46 % / Description: Rod crystals
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 28.7% (w/v) PEG 1500, 0.1 M bis-Tris chloride. Protein concentration 5mg/mL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 19, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.85→41.08 Å / Num. obs: 31937 / % possible obs: 99.7 % / Redundancy: 5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.1
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 5 % / Rmerge(I) obs: 1.08 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(1.11_2567: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K5B

4k5b


Resolution: 1.85→33.947 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2373 1587 4.97 %
Rwork0.2059 --
obs0.2074 31910 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→33.947 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2956 0 118 172 3246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043109
X-RAY DIFFRACTIONf_angle_d0.6254147
X-RAY DIFFRACTIONf_dihedral_angle_d23.3231799
X-RAY DIFFRACTIONf_chiral_restr0.038420
X-RAY DIFFRACTIONf_plane_restr0.003539
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90970.37681500.31762714X-RAY DIFFRACTION100
1.9097-1.9780.31641320.28672748X-RAY DIFFRACTION100
1.978-2.05720.30261540.25282782X-RAY DIFFRACTION100
2.0572-2.15080.28371490.22582717X-RAY DIFFRACTION100
2.1508-2.26410.26011300.21732773X-RAY DIFFRACTION100
2.2641-2.4060.21781450.21142744X-RAY DIFFRACTION100
2.406-2.59170.22261320.20172782X-RAY DIFFRACTION100
2.5917-2.85230.21181300.19662789X-RAY DIFFRACTION100
2.8523-3.26480.24411400.19512764X-RAY DIFFRACTION99
3.2648-4.11220.20231510.17392747X-RAY DIFFRACTION99
4.1122-33.95220.21061740.18222763X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 15.7199 Å / Origin y: -25.3708 Å / Origin z: 0.3265 Å
111213212223313233
T0.0569 Å2-0.008 Å20.0092 Å2-0.0617 Å2-0.0038 Å2--0.0739 Å2
L-0.132 °2-0.0401 °20.0176 °2-0.1797 °20.3013 °2--0.5009 °2
S-0.0072 Å °-0.0192 Å °0.0051 Å °-0.0092 Å °0.0388 Å °-0.1117 Å °-0.0176 Å °0.0369 Å °0.0023 Å °
Refinement TLS groupSelection details: all

+
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