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- PDB-7jmt: Crystal structure of schistosome BCL-2 bound to ABT-737 -

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Basic information

Entry
Database: PDB / ID: 7jmt
TitleCrystal structure of schistosome BCL-2 bound to ABT-737
ComponentsBCL-2 protein
KeywordsAPOPTOSIS
Function / homology
Function and homology information


BH domain binding / negative regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / release of cytochrome c from mitochondria / intrinsic apoptotic signaling pathway in response to DNA damage / regulation of apoptotic process / mitochondrial outer membrane / protein heterodimerization activity / protein homodimerization activity
Similarity search - Function
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
Similarity search - Domain/homology
Chem-N3C / Bcl-2 Bcl-2 homology region 1-3 domain-containing protein / SJCHGC06286 protein
Similarity search - Component
Biological speciesSchistosoma japonicum (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsSmith, N.A. / Smith, B.J. / Lee, E.F. / Colman, P.M. / Fairlie, W.D.
Funding support Australia, 3items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1135421 Australia
National Health and Medical Research Council (NHMRC, Australia)1143974 Australia
National Health and Medical Research Council (NHMRC, Australia)1002227 Australia
CitationJournal: Acs Infect Dis. / Year: 2021
Title: Optimization of Benzothiazole and Thiazole Hydrazones as Inhibitors of Schistosome BCL-2.
Authors: Nguyen, W. / Lee, E.F. / Evangelista, M. / Lee, M. / Harris, T.J. / Colman, P.M. / Smith, N.A. / Williams, L.B. / Jarman, K.E. / Lowes, K.N. / Haeberli, C. / Keiser, J. / Smith, B.J. / ...Authors: Nguyen, W. / Lee, E.F. / Evangelista, M. / Lee, M. / Harris, T.J. / Colman, P.M. / Smith, N.A. / Williams, L.B. / Jarman, K.E. / Lowes, K.N. / Haeberli, C. / Keiser, J. / Smith, B.J. / Fairlie, W.D. / Sleebs, B.E.
History
DepositionAug 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BCL-2 protein
B: BCL-2 protein
C: BCL-2 protein
D: BCL-2 protein
E: BCL-2 protein
F: BCL-2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,38012
Polymers140,5006
Non-polymers4,8816
Water57632
1
A: BCL-2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2302
Polymers23,4171
Non-polymers8131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BCL-2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2302
Polymers23,4171
Non-polymers8131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: BCL-2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2302
Polymers23,4171
Non-polymers8131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: BCL-2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2302
Polymers23,4171
Non-polymers8131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: BCL-2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2302
Polymers23,4171
Non-polymers8131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: BCL-2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2302
Polymers23,4171
Non-polymers8131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.021, 67.789, 100.907
Angle α, β, γ (deg.)90.000, 118.793, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
BCL-2 protein


Mass: 23416.652 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma japonicum (invertebrata) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5BWX6, UniProt: A0A4Z2CSJ3*PLUS
#2: Chemical
ChemComp-N3C / 4-{4-[(4'-CHLOROBIPHENYL-2-YL)METHYL]PIPERAZIN-1-YL}-N-{[4-({(1R)-3-(DIMETHYLAMINO)-1-[(PHENYLTHIO)METHYL]PROPYL}AMINO)-3-NITROPHENYL]SULFONYL}BENZAMIDE / ABT-737


Mass: 813.427 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C42H45ClN6O5S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.64 Å3/Da / Density % sol: 53.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: sBCL-2:1, 1.6M dipotassium hydrogen phosphate, 0.4M sodium dihydrogen phosphate, 0.2M NaCl, 0.1M imidazole, pH8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.75→88.43 Å / Num. obs: 30852 / % possible obs: 99.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 62.99 Å2 / CC1/2: 0.996 / Net I/σ(I): 6.3
Reflection shellResolution: 2.75→2.88 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 4063 / CC1/2: 0.364 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QBR

3qbr


Resolution: 2.75→86.47 Å / SU ML: 0.5125 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.5273
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.255 1547 5.02 %
Rwork0.2336 29244 -
obs0.2347 30791 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.82 Å2
Refinement stepCycle: LAST / Resolution: 2.75→86.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7451 0 336 32 7819
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01237959
X-RAY DIFFRACTIONf_angle_d1.958310806
X-RAY DIFFRACTIONf_chiral_restr0.08481222
X-RAY DIFFRACTIONf_plane_restr0.00761357
X-RAY DIFFRACTIONf_dihedral_angle_d21.23042784
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.840.41031450.37392618X-RAY DIFFRACTION98.33
2.84-2.940.33341120.33812651X-RAY DIFFRACTION98.71
2.94-3.060.39041320.33582641X-RAY DIFFRACTION98.82
3.06-3.20.3451310.29492650X-RAY DIFFRACTION98.72
3.2-3.370.2781410.2752631X-RAY DIFFRACTION98.79
3.37-3.580.28121780.23762629X-RAY DIFFRACTION99.22
3.58-3.850.2411960.22422583X-RAY DIFFRACTION99.18
3.85-4.240.24151100.19412699X-RAY DIFFRACTION99.26
4.24-4.850.18891100.17992711X-RAY DIFFRACTION99.33
4.85-6.110.20941700.2162655X-RAY DIFFRACTION99.3
6.12-86.470.22881220.21682776X-RAY DIFFRACTION98.98

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