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- PDB-3ilb: Crystal structure of mouse Bcl-xl mutant (R139A) at pH 6.0 -

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Entry
Database: PDB / ID: 3ilb
TitleCrystal structure of mouse Bcl-xl mutant (R139A) at pH 6.0
ComponentsBcl-2-like protein 1
KeywordsAPOPTOSIS / BH3 domain / Bcl-2 / Membrane / Mitochondrion / Transmembrane
Function / homology
Function and homology information


The NLRP1 inflammasome / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / RAS processing / apoptotic process in bone marrow cell / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / negative regulation of dendritic cell apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway ...The NLRP1 inflammasome / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / RAS processing / apoptotic process in bone marrow cell / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / negative regulation of dendritic cell apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / negative regulation of execution phase of apoptosis / fertilization / regulation of growth / regulation of mitochondrial membrane permeability / Bcl-2 family protein complex / response to cycloheximide / cellular response to alkaloid / hepatocyte apoptotic process / negative regulation of release of cytochrome c from mitochondria / negative regulation of reproductive process / negative regulation of developmental process / germ cell development / BH3 domain binding / ectopic germ cell programmed cell death / negative regulation of protein localization to plasma membrane / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / response to cytokine / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / regulation of cytokinesis / epithelial cell proliferation / mitochondrion organization / cellular response to amino acid stimulus / mitochondrial membrane / response to radiation / cellular response to gamma radiation / response to virus / synaptic vesicle membrane / intrinsic apoptotic signaling pathway in response to DNA damage / male gonad development / neuron apoptotic process / spermatogenesis / nuclear membrane / defense response to virus / negative regulation of neuron apoptotic process / in utero embryonic development / mitochondrial outer membrane / mitochondrial inner membrane / mitochondrial matrix / positive regulation of apoptotic process / apoptotic process / centrosome / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum / mitochondrion / identical protein binding / membrane / cytosol
Similarity search - Function
Apoptosis regulator, Bcl-X / Apoptosis regulator, Bcl-2/ BclX / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / Blc2-like / Apoptosis Regulator Bcl-x ...Apoptosis regulator, Bcl-X / Apoptosis regulator, Bcl-2/ BclX / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Bcl-2-like protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsPriyadarshi, A. / Hwang, K.Y.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2010
Title: Structural insights into mouse anti-apoptotic Bcl-xl reveal affinity for Beclin 1 and gossypol.
Authors: Priyadarshi, A. / Roy, A. / Kim, K.S. / Kim, E.E. / Hwang, K.Y.
History
DepositionAug 7, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 2013Group: Database references
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

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Assembly

Deposited unit
A: Bcl-2-like protein 1
N: Bcl-2-like protein 1


Theoretical massNumber of molelcules
Total (without water)43,9402
Polymers43,9402
Non-polymers00
Water18010
1
A: Bcl-2-like protein 1


Theoretical massNumber of molelcules
Total (without water)21,9701
Polymers21,9701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
N: Bcl-2-like protein 1


Theoretical massNumber of molelcules
Total (without water)21,9701
Polymers21,9701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.497, 34.721, 95.552
Angle α, β, γ (deg.)90.00, 89.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Bcl-2-like protein 1


Mass: 21970.094 Da / Num. of mol.: 2 / Fragment: UNP residues 1-196 / Mutation: R139A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bcl-xl, Bcl2l, Bcl2l1, Bclx / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q64373
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 1.98 Å3/Da / Density % sol: 37.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.2M Ammonium sulphate, 0.3M Lithium sulphate, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 8, 2008 / Details: mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. all: 13028 / Num. obs: 12366 / % possible obs: 91.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 39.9 Å2 / Rmerge(I) obs: 0.14 / Rsym value: 0.34 / Net I/σ(I): 25
Reflection shellResolution: 2.38→2.47 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 4.5 / Num. unique all: 1274 / Rsym value: 0.34 / % possible all: 91.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PQ0

1pq0


Resolution: 2.38→35.45 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.859 / SU B: 8.525 / SU ML: 0.207 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.563 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2934 654 5 %RANDOM
Rwork0.23661 ---
all0.2394 13028 --
obs0.2394 12366 91.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.912 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20.03 Å2
2---0.2 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.38→35.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2416 0 0 10 2426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0212474
X-RAY DIFFRACTIONr_angle_refined_deg1.7681.9243352
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9265298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14623.906128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.30715394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7731516
X-RAY DIFFRACTIONr_chiral_restr0.1260.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021926
X-RAY DIFFRACTIONr_mcbond_it1.0641.51492
X-RAY DIFFRACTIONr_mcangle_it2.00922382
X-RAY DIFFRACTIONr_scbond_it2.8923982
X-RAY DIFFRACTIONr_scangle_it4.5634.5970
LS refinement shellResolution: 2.377→2.439 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 49 -
Rwork0.262 729 -
obs--73.95 %

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