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- PDB-6v4m: Trichuris suis BCL-2 -

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Basic information

Entry
Database: PDB / ID: 6v4m
TitleTrichuris suis BCL-2
ComponentsBCL-2
KeywordsAPOPTOSIS / BCL-2 / helical bundle
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 / protein homodimerization activity
Similarity search - Function
Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / 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
Bcl-2 Bcl-2 homology region 1-3 domain-containing 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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