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- PDB-7ccl: Crystal structure of human BFK -

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Basic information

Entry
Database: PDB / ID: 7ccl
TitleCrystal structure of human BFK
ComponentsBcl-2-like protein 15
KeywordsAPOPTOSIS / BCL-2 family kin
Function / homology
Function and homology information


regulation of apoptotic process / apoptotic process / nucleus / cytosol
Similarity search - Function
Bcl-2-like protein 15 / Blc2-like / Apoptosis Regulator Bcl-x / Bcl-2-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Bcl-2-like protein 15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsJang, D.M. / Oh, E.K. / Han, B.W.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2011-0030001 Korea, Republic Of
CitationJournal: To Be Published
Title: Structural analyses on human BFK, a Novel BCL-2 Family Member.
Authors: Jang, D.M. / Oh, E.K. / Han, B.W.
History
DepositionJun 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Data collection / Category: pdbx_reflns_twin / Item: _pdbx_reflns_twin.diffrn_id
Revision 1.2Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bcl-2-like protein 15
B: Bcl-2-like protein 15
C: Bcl-2-like protein 15


Theoretical massNumber of molelcules
Total (without water)59,7223
Polymers59,7223
Non-polymers00
Water19811
1
A: Bcl-2-like protein 15


Theoretical massNumber of molelcules
Total (without water)19,9071
Polymers19,9071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bcl-2-like protein 15


Theoretical massNumber of molelcules
Total (without water)19,9071
Polymers19,9071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bcl-2-like protein 15


Theoretical massNumber of molelcules
Total (without water)19,9071
Polymers19,9071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.500, 116.500, 27.630
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Bcl-2-like protein 15 / BFK / Bcl2-L-15


Mass: 19907.430 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2L15, C1orf178 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5TBC7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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

Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M Bis-Tris pH 5.5, 28% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97957 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.5386
pseudo-merohedral21-h,-k,l20.4614
ReflectionResolution: 2.7→30 Å / Num. obs: 11459 / % possible obs: 99.3 % / Redundancy: 3.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Net I/σ(I): 13.5
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.809 / Mean I/σ(I) obs: 1.96 / Num. unique obs: 878 / CC1/2: 0.599 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CCM

7ccm


Resolution: 2.7→29.125 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 9.866 / SU ML: 0.212 / Cross valid method: FREE R-VALUE / ESU R Free: 0.061
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1901 578 5.055 %
Rwork0.1579 10856 -
all0.16 --
obs-11434 99.331 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 64.349 Å2
Baniso -1Baniso -2Baniso -3
1-17.984 Å20 Å20 Å2
2--17.984 Å20 Å2
3----35.968 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29.125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3306 0 0 11 3317
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0133350
X-RAY DIFFRACTIONr_bond_other_d0.0030.0173114
X-RAY DIFFRACTIONr_angle_refined_deg1.1671.6274534
X-RAY DIFFRACTIONr_angle_other_deg1.0351.5647238
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0665428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.77425.031163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81615582
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.141512
X-RAY DIFFRACTIONr_chiral_restr0.0220.2460
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023755
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02633
X-RAY DIFFRACTIONr_nbd_refined0.1560.2716
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1570.22650
X-RAY DIFFRACTIONr_nbtor_refined0.1330.21643
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21321
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.270
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0810.211
X-RAY DIFFRACTIONr_nbd_other0.1380.291
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0520.27
X-RAY DIFFRACTIONr_mcbond_it0.6477.0541730
X-RAY DIFFRACTIONr_mcbond_other0.6477.0541729
X-RAY DIFFRACTIONr_mcangle_it1.22710.5752152
X-RAY DIFFRACTIONr_mcangle_other1.22710.5752153
X-RAY DIFFRACTIONr_scbond_it0.3117.0691620
X-RAY DIFFRACTIONr_scbond_other0.3117.0681618
X-RAY DIFFRACTIONr_scangle_it0.66910.5822382
X-RAY DIFFRACTIONr_scangle_other0.66910.5822382
X-RAY DIFFRACTIONr_lrange_it2.82984.3323703
X-RAY DIFFRACTIONr_lrange_other2.82884.343704
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.269560.235797X-RAY DIFFRACTION97.9334
2.77-2.8450.274380.232744X-RAY DIFFRACTION100
2.845-2.9270.286220.211794X-RAY DIFFRACTION100
2.927-3.0160.208220.212753X-RAY DIFFRACTION100
3.016-3.1140.307300.205736X-RAY DIFFRACTION98.8387
3.114-3.2220.25440.181668X-RAY DIFFRACTION99.5804
3.222-3.3420.167380.197682X-RAY DIFFRACTION100
3.342-3.4760.158300.173662X-RAY DIFFRACTION99.4253
3.476-3.6290.211400.155570X-RAY DIFFRACTION100
3.629-3.8030.228340.14593X-RAY DIFFRACTION99.8408
3.803-4.0050.209360.139563X-RAY DIFFRACTION98.8449
4.005-4.2440.191220.144515X-RAY DIFFRACTION100
4.244-4.530.134240.123522X-RAY DIFFRACTION99.635
4.53-4.8840.196300.139441X-RAY DIFFRACTION97.7178
4.884-5.3360.279350.157429X-RAY DIFFRACTION99.7849
5.336-5.9420.082160.187389X-RAY DIFFRACTION97.5904
5.942-6.8170.139180.162343X-RAY DIFFRACTION97.832
6.817-8.2430.127220.117274X-RAY DIFFRACTION99.6633
8.243-11.2410.125140.094230X-RAY DIFFRACTION99.5918
11.241-29.1250.15870.185151X-RAY DIFFRACTION99.3711

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