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- PDB-5w63: Crystal structure of channel catfish BAX -

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Basic information

Entry
Database: PDB / ID: 5w63
TitleCrystal structure of channel catfish BAX
ComponentsApoptosis regulator bax
KeywordsAPOPTOSIS / BAX / monomer / catfish
Function / homologyBcl-2 family / Bcl2-like / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily / regulation of apoptotic process / apoptotic process / apoptosis regulator BAX
Function and homology information
Biological speciesIctalurus punctatus (channel catfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.436 Å
AuthorsRobin, A.Y. / Colman, P.M. / Czabotar, P.E. / Luo, C.S.
CitationJournal: Structure / Year: 2018
Title: Ensemble Properties of Bax Determine Its Function.
Authors: Robin, A.Y. / Iyer, S. / Birkinshaw, R.W. / Sandow, J. / Wardak, A. / Luo, C.S. / Shi, M. / Webb, A.I. / Czabotar, P.E. / Kluck, R.M. / Colman, P.M.
History
DepositionJun 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Sep 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 17, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.4Oct 4, 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: Apoptosis regulator bax
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9128
Polymers21,3751
Non-polymers5367
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Apoptosis regulator bax
hetero molecules

A: Apoptosis regulator bax
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,82416
Polymers42,7512
Non-polymers1,07314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_566x,-y+1,-z+11
Buried area6500 Å2
ΔGint-109 kcal/mol
Surface area16680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.963, 58.490, 71.984
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-207-

EDO

21A-304-

HOH

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Components

#1: Protein Apoptosis regulator bax


Mass: 21375.400 Da / Num. of mol.: 1 / Mutation: C51S, C117S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ictalurus punctatus (channel catfish) / Gene: BAX / Production host: Escherichia coli (E. coli) / References: UniProt: E3TFZ1
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.41 Å3/Da / Density % sol: 48.99 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, bis-TRIS, ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.436→40.485 Å / Num. obs: 8066 / % possible obs: 99 % / Redundancy: 6.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.1523 / Net I/σ(I): 12.86
Reflection shellResolution: 2.436→2.523 Å / Rmerge(I) obs: 0.619 / CC1/2: 0.784

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W60

5w60


Resolution: 2.436→40.485 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.35
RfactorNum. reflection% reflection
Rfree0.2541 404 5.01 %
Rwork0.1731 --
obs0.1771 8066 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.436→40.485 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1402 0 31 64 1497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071466
X-RAY DIFFRACTIONf_angle_d0.8171987
X-RAY DIFFRACTIONf_dihedral_angle_d14.601845
X-RAY DIFFRACTIONf_chiral_restr0.047226
X-RAY DIFFRACTIONf_plane_restr0.004247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4361-2.78860.31241290.21172437X-RAY DIFFRACTION97
2.7886-3.5130.30321340.18452550X-RAY DIFFRACTION100
3.513-40.49070.19971410.15152675X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0856-0.00320.07150.00610.00560.0854-0.0171-0.0298-0.0906-0.01070.0645-0.0077-0.0281-0.27930.06130.03190.0010.04570.2495-0.02880.12354.952826.067519.5329
2-0.00110.0013-00.0050.00150.00180.00960.0542-0.00030.0882-0.0029-0.0416-0.0269-0.00470.00010.33080.11720.10630.34280.0270.30917.23140.508213.8774
30.25650.00230.21120.1115-0.0640.2175-0.0726-0.16940.05430.13040.0598-0.0324-0.1643-0.2741-0.03220.0675-0.0421-0.00090.06560.00260.073310.914133.596222.0136
40.1384-0.051-0.00170.00550.00360.07730.03250.0403-0.01790.0131-0.0505-0.0090.0594-0.051800.0908-0.00870.00830.0596-0.01910.085115.554824.034614.1517
50.09680.0344-0.04770.1214-0.01450.0209-0.0707-0.0169-0.1392-0.25610.01730.03730.10190.0418-0.13610.064-0.0480.01380.0303-0.04460.059723.718227.792546.8157
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 41 )
3X-RAY DIFFRACTION3chain 'A' and (resid 42 through 80 )
4X-RAY DIFFRACTION4chain 'A' and (resid 81 through 159 )
5X-RAY DIFFRACTION5chain 'A' and (resid 160 through 186 )

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