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- PDB-5af3: X-RAY CRYSTAL STRUCTURE OF RV2018 FROM MYCOBACTERIUM TUBERCULOSIS -

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Basic information

Entry
Database: PDB / ID: 5af3
TitleX-RAY CRYSTAL STRUCTURE OF RV2018 FROM MYCOBACTERIUM TUBERCULOSIS
ComponentsVAPBC49
KeywordsDNA BINDING / MYCOBACTERIUM TUBERCULOSIS / TA SYSTEM
Function / homologyPutative antitoxin VapB45-like / Protein of unknown function DUF433 / Protein of unknown function (DUF433) / Homeobox-like domain superfamily / Putative antitoxin VapB45
Function and homology information
Biological speciesMYCOBACTERIUM TUBERCULOSIS H37RV (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.78 Å
AuthorsHolton, S.J. / Wilmanns, M.
CitationJournal: To be Published
Title: Crystal Structure and DNA Binding Ability of Myco Tuberculosis Vapbc49 Anti-Toxin Protein Bacterium
Authors: Holton, S.J. / Pogenberg, V. / Iborra, V. / Wilmanns, M.
History
DepositionJan 18, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VAPBC49
B: VAPBC49
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4693
Polymers52,3772
Non-polymers921
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-9.9 kcal/mol
Surface area19440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.935, 81.935, 75.361
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein VAPBC49


Mass: 26188.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS H37RV (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O53464
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.89 Å3/Da / Density % sol: 57.13 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: BW7A / Wavelength: 0.9792
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.77→40.96 Å / Num. obs: 53660 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 3.81 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.73
Reflection shellResolution: 1.77→1.87 Å / Redundancy: 3.55 % / Rmerge(I) obs: 0.46 / % possible all: 83.5

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Processing

SoftwareName: REFMAC / Version: 5.2.0005 / Classification: refinement
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 1.78→70.89 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.801 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25421 2726 5.1 %RANDOM
Rwork0.21048 ---
obs0.21264 50907 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20.38 Å20 Å2
2--0.76 Å20 Å2
3----1.14 Å2
Refinement stepCycle: LAST / Resolution: 1.78→70.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3304 0 6 289 3599

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