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- PDB-5twa: Crystal structure of Geodia cydonium BHP2 in complex with Lubomir... -

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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


regulation of apoptotic process / membrane => GO:0016020 / positive regulation of apoptotic process / apoptotic process
Similarity search - Function
Apoptosis regulator BAK / 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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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 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

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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

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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

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