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- PDB-5vmn: Crystal structure of grouper iridovirus GIV66 -

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Basic information

Entry
Database: PDB / ID: 5vmn
TitleCrystal structure of grouper iridovirus GIV66
ComponentsBak protein
KeywordsVIRAL PROTEIN / Apoptosis / Bcl-2 / iridovirus / grouper
Function / homologysymbiont-mediated suppression of host apoptosis / 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 / NITRATE ION / Bak protein
Function and homology information
Biological speciesGrouper iridovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsBanjara, S. / Kvansakul, M.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Grouper iridovirus GIV66 is a Bcl-2 protein that inhibits apoptosis by exclusively sequestering Bim.
Authors: Banjara, S. / Mao, J. / Ryan, T.M. / Caria, S. / Kvansakul, M.
History
DepositionApr 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Bak protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,81215
Polymers14,9441
Non-polymers86814
Water1,910106
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: SAXS, Dimer as shown by SEC-SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.033, 68.033, 85.824
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-346-

HOH

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Components

#1: Protein Bak protein


Mass: 14943.972 Da / Num. of mol.: 1 / Fragment: UNP residues 1-127
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Grouper iridovirus / Gene: GIV66 / Plasmid: pGEX-6P3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5GAF0
#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: NO3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 3.32 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 4.0 M sodium nitrate with 0.1 M sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.65→42.91 Å / Num. obs: 24871 / % possible obs: 99.9 % / Redundancy: 10 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Net I/σ(I): 24.8
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 11.1 % / Rmerge(I) obs: 2.395 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1219 / CC1/2: 0.396 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→41.964 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2142 1210 4.87 %
Rwork0.1833 --
obs0.1847 24871 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→41.964 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms992 0 56 106 1154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011052
X-RAY DIFFRACTIONf_angle_d1.0171403
X-RAY DIFFRACTIONf_dihedral_angle_d16.821611
X-RAY DIFFRACTIONf_chiral_restr0.051156
X-RAY DIFFRACTIONf_plane_restr0.007183
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.71610.36171270.32562589X-RAY DIFFRACTION100
1.7161-1.79420.30511540.28822554X-RAY DIFFRACTION100
1.7942-1.88880.28131270.23092595X-RAY DIFFRACTION100
1.8888-2.00710.24981370.19952593X-RAY DIFFRACTION100
2.0071-2.16210.21931150.16542598X-RAY DIFFRACTION100
2.1621-2.37960.16461450.16152614X-RAY DIFFRACTION100
2.3796-2.72390.18411320.16022646X-RAY DIFFRACTION100
2.7239-3.43160.20351240.1772686X-RAY DIFFRACTION100
3.4316-41.97740.21751490.18152786X-RAY DIFFRACTION99
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)
12.9485-2.97490.85993.1739-0.63910.51710.1896-0.0355-0.73110.09740.3308-0.15260.7409-0.2471-0.49610.5029-0.0189-0.08890.4680.05910.56164.503-25.850514.7089
25.0235-0.89740.6622.1402-0.64451.531-0.2213-0.49530.38570.1920.1499-0.101-0.1329-0.01240.07820.2570.0005-0.01470.2705-0.00530.25290.0482-9.8649.9029
35.1384-1.16680.20242.16960.1693.56070.0482-0.0905-0.41480.0033-0.02030.11770.21550.0167-0.02450.212-0.0084-0.0460.20220.04560.2455-0.3184-18.74815.4437
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -4 through 11 )
2X-RAY DIFFRACTION2chain 'A' and (resid 12 through 47 )
3X-RAY DIFFRACTION3chain 'A' and (resid 48 through 120 )

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