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- PDB-5y06: Structural characterization of msmeg_4306 from Mycobacterium smegmatis -

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Basic information

Entry
Database: PDB / ID: 5y06
TitleStructural characterization of msmeg_4306 from Mycobacterium smegmatis
Componentsmsmeg_4306
KeywordsUNKNOWN FUNCTION / coiled coil helix / zinc ribbon / hypothetical / zinc-SAD
Function / homology
Function and homology information


C4-type zinc ribbon domain / : / : / C4-type zinc ribbon domain / CT398-like coiled coil hairpin domain / Helix Hairpins - #1490 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.606 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 1.1Nov 22, 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

Downloads & links

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Assembly

Deposited unit
A: msmeg_4306
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6953
Polymers29,5381
Non-polymers1582
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-1 kcal/mol
Surface area14440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.600, 76.600, 84.811
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.65 Å3/Da / Density % sol: 53 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 7, 2016 / Details: Mirror
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.59→66.34 Å / Num. obs: 9152 / % possible obs: 98.2 % / Redundancy: 8.4 % / Biso Wilson estimate: 51 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.034 / Net I/σ(I): 16.4
Reflection shellResolution: 2.59→2.71 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.621 / Num. unique obs: 955 / CC1/2: 0.7 / Rpim(I) all: 0.23 / % possible all: 85.1

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Processing

Software
NameVersionClassification
PHENIXdev_2614refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y05

5y05


Resolution: 2.606→66.338 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.65
RfactorNum. reflection% reflection
Rfree0.2713 460 5.06 %
Rwork0.2402 --
obs0.2419 9097 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 70.8 Å2
Refinement stepCycle: LAST / Resolution: 2.606→66.338 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1732 0 7 14 1753
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0011741
X-RAY DIFFRACTIONf_angle_d0.3632350
X-RAY DIFFRACTIONf_dihedral_angle_d1.9071097
X-RAY DIFFRACTIONf_chiral_restr0.029282
X-RAY DIFFRACTIONf_plane_restr0.001321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6064-2.98350.40421530.33382782X-RAY DIFFRACTION98
2.9835-3.75890.32731530.26862865X-RAY DIFFRACTION100
3.7589-66.35910.21181540.20282990X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 133.3993 Å / Origin y: 38.516 Å / Origin z: 87.4645 Å
111213212223313233
T0.3746 Å20.0036 Å20.0096 Å2-0.2582 Å20.0488 Å2--0.263 Å2
L3.8491 °22.6259 °21.2502 °2-3.0089 °21.3752 °2--1.3945 °2
S0.1132 Å °-0.2216 Å °0.1703 Å °0.0304 Å °-0.2784 Å °0.1552 Å °-0.1327 Å °-0.1002 Å °0.1256 Å °
Refinement TLS groupSelection details: all

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