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- PDB-5y05: Structural characterization of msmeg_4306 from Mycobacterium smegmatis -

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Basic information

Entry
Database: PDB / ID: 5y05
TitleStructural characterization of msmeg_4306 from Mycobacterium smegmatis
Componentsmsmeg_4306
KeywordsUNKNOWN FUNCTION / coiled coil helix / zinc ribbon / hypothetical / zinc-SAD
Function / homologyC4-type zinc ribbon domain / C4-type zinc ribbon domain / C4-type zinc ribbon domain-containing protein
Function and homology information
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.799 Å
AuthorsKumar, A. / Karthikeyan, S.
Funding support India, 1items
OrganizationGrant numberCountry
CSIR, Government of IndiaBSC0104, BSC0210 India
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Crystal structure of the MSMEG_4306 gene product from Mycobacterium smegmatis
Authors: Kumar, A. / Karthikeyan, S.
History
DepositionJul 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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: msmeg_4306
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6032
Polymers29,5381
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14360 Å2
Unit cell
Length a, b, c (Å)77.137, 77.137, 85.791
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein msmeg_4306 / Uncharacterized protein


Mass: 29537.975 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_4306 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0R095
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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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: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG 8000, 5% PEG 2000 MME, 0.1 M Tris-Hcl pH 8.5, 0.1 M magnesium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.28198 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 22, 2016
RadiationMonochromator: SI III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28198 Å / Relative weight: 1
ReflectionResolution: 2.799→50 Å / Num. obs: 7606 / % possible obs: 100 % / Redundancy: 21.2 % / Biso Wilson estimate: 87.31 Å2 / CC1/2: 0.966 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.02 / Net I/σ(I): 47.45
Reflection shellResolution: 2.799→2.9 Å / Redundancy: 18.8 % / Rmerge(I) obs: 1.439 / Mean I/σ(I) obs: 1.93 / Num. unique obs: 744 / CC1/2: 0.952 / Rpim(I) all: 0.333 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_2614refinement
HKL-2000data reduction
HKL-2000data scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.799→38.569 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 34.29
RfactorNum. reflection% reflection
Rfree0.3118 376 4.95 %
Rwork0.2581 --
obs0.2605 7602 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 91.7 Å2
Refinement stepCycle: LAST / Resolution: 2.799→38.569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1666 0 1 0 1667
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0011670
X-RAY DIFFRACTIONf_angle_d0.3082261
X-RAY DIFFRACTIONf_dihedral_angle_d9.0091047
X-RAY DIFFRACTIONf_chiral_restr0.029274
X-RAY DIFFRACTIONf_plane_restr0.002311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7992-3.20410.36111060.32072386X-RAY DIFFRACTION100
3.2041-4.03610.3311430.27342350X-RAY DIFFRACTION100
4.0361-38.57210.2921270.2422490X-RAY DIFFRACTION100

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