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- PDB-4jkz: Crystal structure of ms6564 from mycobacterium smegmatis -

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Basic information

Entry
Database: PDB / ID: 4jkz
TitleCrystal structure of ms6564 from mycobacterium smegmatis
ComponentsTranscriptional regulator, TetR familyTranscriptional regulation
KeywordsTRANSCRIPTION / transcriptional regulator
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Tetracyclin repressor-like, C-terminal domain / Tetracyclin repressor-like, C-terminal domain / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional regulator, TetR family protein
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsYang, S.F. / Gao, Z.Q. / He, Z.G. / Dong, Y.H.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural basis for interaction between Mycobacterium smegmatis Ms6564, a TetR family master regulator, and its target DNA.
Authors: Yang, S. / Gao, Z. / Li, T. / Yang, M. / Zhang, T. / Dong, Y. / He, Z.G.
History
DepositionMar 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Aug 24, 2022Group: Database references
Category: citation / citation_author ...citation / citation_author / database_2 / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator, TetR family


Theoretical massNumber of molelcules
Total (without water)21,0861
Polymers21,0861
Non-polymers00
Water1,928107
1
A: Transcriptional regulator, TetR family

A: Transcriptional regulator, TetR family


Theoretical massNumber of molelcules
Total (without water)42,1722
Polymers42,1722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area2630 Å2
ΔGint-18 kcal/mol
Surface area17240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.263, 118.289, 49.984
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Transcriptional regulator, TetR family / Transcriptional regulation / Transcriptional regulator / TetR family protein


Mass: 21086.029 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_6564, MSMEI_6387 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0R6I8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.04 Å3/Da / Density % sol: 39.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M sodium citrate, 0.1M HEPES, 30% MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 15, 2012
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 16377 / Num. obs: 16377 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 50.4
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 2.27 / % possible all: 95.7

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Processing

Software
NameVersionClassification
MAR345data collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→29.572 Å / SU ML: 0.23 / σ(F): 1.37 / Phase error: 26.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.263 824 5.04 %
Rwork0.2126 --
obs0.215 16361 99.56 %
all-16377 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-18.3899 Å20 Å2-0 Å2
2--9.6797 Å2-0 Å2
3---13.5799 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.572 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1361 0 0 107 1468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071378
X-RAY DIFFRACTIONf_angle_d1.0481865
X-RAY DIFFRACTIONf_dihedral_angle_d14.869509
X-RAY DIFFRACTIONf_chiral_restr0.066220
X-RAY DIFFRACTIONf_plane_restr0.004242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.91250.33761380.27392497X-RAY DIFFRACTION98
1.9125-2.06020.2921290.23592560X-RAY DIFFRACTION100
2.0602-2.26740.26381310.20642572X-RAY DIFFRACTION100
2.2674-2.59530.2471490.20522572X-RAY DIFFRACTION100
2.5953-3.26920.26761590.22192595X-RAY DIFFRACTION100
3.2692-29.57620.25151180.20172741X-RAY DIFFRACTION100

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