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- PDB-7ccm: Crystal structure of selenomethionine-derived human BFK -

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Basic information

Entry
Database: PDB / ID: 7ccm
TitleCrystal structure of selenomethionine-derived 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 / SAD / Resolution: 2.45 Å
AuthorsOh, E.K. / Jang, D.M. / 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 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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 / _pdbx_entry_details.has_protein_modification

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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)60,7073
Polymers60,7073
Non-polymers00
Water34219
1
A: Bcl-2-like protein 15


Theoretical massNumber of molelcules
Total (without water)20,2361
Polymers20,2361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bcl-2-like protein 15


Theoretical massNumber of molelcules
Total (without water)20,2361
Polymers20,2361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bcl-2-like protein 15


Theoretical massNumber of molelcules
Total (without water)20,2361
Polymers20,2361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.156, 116.156, 27.679
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 / Bcl2-L-15


Mass: 20235.693 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.: 19 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 0.97918 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 15406 / % possible obs: 99.1 % / Redundancy: 3.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.071 / Net I/σ(I): 12.32
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 2 % / Rmerge(I) obs: 0.784 / Mean I/σ(I) obs: 1.06 / Num. unique obs: 708 / CC1/2: 0.803 / % possible all: 90.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.45→38.05 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.904 / WRfactor Rfree: 0.236 / WRfactor Rwork: 0.198 / SU B: 12.053 / SU ML: 0.267 / Average fsc free: 0.8679 / Average fsc work: 0.8956 / Cross valid method: FREE R-VALUE / ESU R Free: 0.354
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2538 629 4.955 %
Rwork0.2124 12064 -
all0.214 --
obs-12693 82.561 %
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: 39.143 Å2
Baniso -1Baniso -2Baniso -3
1-0.183 Å20.092 Å20 Å2
2--0.183 Å2-0 Å2
3----0.595 Å2
Refinement stepCycle: LAST / Resolution: 2.45→38.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3310 0 0 19 3329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133354
X-RAY DIFFRACTIONr_bond_other_d0.0050.0173117
X-RAY DIFFRACTIONr_angle_refined_deg1.1191.6354539
X-RAY DIFFRACTIONr_angle_other_deg1.0561.5637245
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6395429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.75625.031163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01815537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.2211512
X-RAY DIFFRACTIONr_chiral_restr0.0240.2460
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023762
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02634
X-RAY DIFFRACTIONr_nbd_refined0.1590.2693
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1540.22680
X-RAY DIFFRACTIONr_nbtor_refined0.1330.21669
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21183
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1050.269
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0840.216
X-RAY DIFFRACTIONr_nbd_other0.1360.295
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0710.27
X-RAY DIFFRACTIONr_mcbond_it0.9644.2141734
X-RAY DIFFRACTIONr_mcbond_other0.9644.2141733
X-RAY DIFFRACTIONr_mcangle_it1.7236.3132157
X-RAY DIFFRACTIONr_mcangle_other1.7226.3132158
X-RAY DIFFRACTIONr_scbond_it1.3784.3151620
X-RAY DIFFRACTIONr_scbond_other1.3784.3141618
X-RAY DIFFRACTIONr_scangle_it2.1466.4032382
X-RAY DIFFRACTIONr_scangle_other2.1466.4032382
X-RAY DIFFRACTIONr_lrange_it3.19950.6723664
X-RAY DIFFRACTIONr_lrange_other3.19950.683665
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.5130.266110.302338X-RAY DIFFRACTION29.4019
2.513-2.5820.377300.286321X-RAY DIFFRACTION32.7731
2.582-2.6570.22790.256459X-RAY DIFFRACTION43.7383
2.657-2.7380.33180.26666X-RAY DIFFRACTION64.2253
2.738-2.8280.301760.267830X-RAY DIFFRACTION91.1469
2.828-2.9270.296500.254901X-RAY DIFFRACTION98.2438
2.927-3.0370.29480.247905X-RAY DIFFRACTION98.9616
3.037-3.160.3440.238855X-RAY DIFFRACTION99.6674
3.16-3.30.287460.235826X-RAY DIFFRACTION100
3.3-3.4610.277510.224790X-RAY DIFFRACTION99.6445
3.461-3.6470.258260.193745X-RAY DIFFRACTION100
3.647-3.8670.236430.183721X-RAY DIFFRACTION99.8693
3.867-4.1320.207180.176668X-RAY DIFFRACTION99.8544
4.132-4.4610.244280.176645X-RAY DIFFRACTION100
4.461-4.8820.176240.18569X-RAY DIFFRACTION99.6639
4.882-5.4520.215450.216505X-RAY DIFFRACTION98.7433
5.452-6.2830.345180.245452X-RAY DIFFRACTION99.7877
6.283-7.6650.207200.22385X-RAY DIFFRACTION100
7.665-10.7150.17180.16312X-RAY DIFFRACTION99.6979
10.715-38.050.39560.242171X-RAY DIFFRACTION100

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