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- PDB-4k5a: Co-crystallization with conformation-specific designed ankyrin re... -

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Basic information

Entry
Database: PDB / ID: 4k5a
TitleCo-crystallization with conformation-specific designed ankyrin repeat proteins explains the conformational flexibility of BCL-W
Components
  • Bcl-2-like protein 2
  • Designed Ankyrin Repeat Protein 013_D12
KeywordsAPOPTOSIS / anti-apoptotic BCL-2 family / BCL-W / crystal structure / ligand binding-competent conformation / DARPins
Function / homology
Function and homology information


Sertoli cell proliferation / Bcl-2 family protein complex / negative regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / intrinsic apoptotic signaling pathway in response to DNA damage / disordered domain specific binding / mitochondrial outer membrane / protein heterodimerization activity / protein homodimerization activity / cytosol
Similarity search - Function
Apoptosis regulator, Bcl-W / 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 / Ankyrin repeat-containing domain / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. ...Apoptosis regulator, Bcl-W / 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 / Ankyrin repeat-containing domain / 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 (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 / Bcl2-like / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Bcl-2-like protein 2
Similarity search - Component
Biological speciesBos taurus (cattle)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsSchilling, J. / Schoeppe, J. / Sauer, E. / Plueckthun, A.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Co-Crystallization with Conformation-Specific Designed Ankyrin Repeat Proteins Explains the Conformational Flexibility of BCL-W
Authors: Schilling, J. / Schoppe, J. / Sauer, E. / Pluckthun, A.
History
DepositionApr 14, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Database references
Revision 1.2Jun 11, 2014Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bcl-2-like protein 2
B: Designed Ankyrin Repeat Protein 013_D12


Theoretical massNumber of molelcules
Total (without water)38,3822
Polymers38,3822
Non-polymers00
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-9 kcal/mol
Surface area15570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.700, 42.600, 76.700
Angle α, β, γ (deg.)90.000, 110.800, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Bcl-2-like protein 2 / Bcl2-L-2 / Apoptosis regulator Bcl-W


Mass: 20194.453 Da / Num. of mol.: 1 / Fragment: UNP residues 2-171 / Mutation: P128V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: BCL2L2 / Plasmid: pPANK / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-blue / References: UniProt: Q1RMX3
#2: Protein Designed Ankyrin Repeat Protein 013_D12


Mass: 18187.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pQIq / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-blue
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THE ENTITY 2 DOES NOT CURRENTLY EXIST.

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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: 2.2 Å3/Da / Density % sol: 44.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8
Details: 0.1M HEPES, 0.2M Li2SO4 , 25% PEG4000, pH 8, vapor diffusion, temperature 277K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionHighest resolution: 1.5 Å / Num. obs: 52907 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.547 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.65
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.5-1.540.4430.3333.5612285399538390.39796.1
1.54-1.580.3640.2854.3912922382736910.33596.4
1.58-1.630.290.2415.313313377336850.28297.7
1.63-1.680.2330.1986.2212793361235470.23398.2
1.68-1.730.2050.1687.1612392356334800.19897.7
1.73-1.790.1780.148.1611614345333910.16698.2
1.79-1.860.1270.1159.9111246329032240.13598
1.86-1.940.1070.09811.9911508318231360.11498.6
1.94-2.020.0860.08213.7610889303830010.09698.8
2.02-2.120.0640.06616.5510537295129220.07899
2.12-2.240.0550.05718.619452275527160.06798.6
2.24-2.370.0450.0520.398765266726170.05998.1
2.37-2.540.0410.04723.478903244424270.05599.3
2.54-2.740.0360.04424.858389233023080.05199.1
2.74-30.0310.03926.937462212721090.04699.2
3-3.350.030.03627.436095194319010.04397.8
3.35-3.870.0230.03333.016076172017010.03998.9
3.87-4.740.0230.03234.195167145414430.03899.2
4.74-6.710.0260.03431.53629115111230.0497.6
6.710.0240.03436.5922666596460.04198

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å39.39 Å
Translation2.5 Å39.39 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
PHENIX1.7.2_869refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→39.393 Å / Occupancy max: 1 / Occupancy min: 0.29 / FOM work R set: 0.8941 / SU ML: 0.38 / σ(F): 2 / Phase error: 17.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1903 2691 5.09 %
Rwork0.1565 --
obs0.1582 52902 98.19 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.642 Å2 / ksol: 0.349 e/Å3
Displacement parametersBiso max: 60.69 Å2 / Biso mean: 19.7008 Å2 / Biso min: 5.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.8284 Å20 Å2-0.0519 Å2
2--0.6295 Å2-0 Å2
3---0.1989 Å2
Refinement stepCycle: LAST / Resolution: 1.5→39.393 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2468 0 0 402 2870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052594
X-RAY DIFFRACTIONf_angle_d0.9373537
X-RAY DIFFRACTIONf_chiral_restr0.065386
X-RAY DIFFRACTIONf_plane_restr0.004473
X-RAY DIFFRACTIONf_dihedral_angle_d12.77929
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.52730.2411260.20682604273096
1.5273-1.55670.25871500.19222552270297
1.5567-1.58840.22971470.18652598274597
1.5884-1.6230.20561320.1782630276298
1.623-1.66070.22291380.16292602274098
1.6607-1.70230.22571430.17112599274297
1.7023-1.74830.21731300.15882647277799
1.7483-1.79970.20891350.14882639277498
1.7997-1.85780.2031600.1372611277198
1.8578-1.92420.20821310.14052650278199
1.9242-2.00130.16471400.14412647278799
2.0013-2.09230.21241720.14752616278899
2.0923-2.20270.17321480.14042650279899
2.2027-2.34060.171370.13922652278998
2.3406-2.52130.17651440.14532662280699
2.5213-2.7750.18511380.15432680281899
2.775-3.17640.18831490.15912692284199
3.1764-4.00130.17951310.14982716284799
4.0013-39.40640.17361400.17672764290498

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