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- PDB-4jl3: Crystal structure of ms6564-dna complex -

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Basic information

Entry
Database: PDB / ID: 4jl3
TitleCrystal structure of ms6564-dna complex
Components
  • (DNA (31-MER)) x 2
  • Transcriptional regulator, TetR familyTranscriptional regulation
KeywordsTRANSCRIPTION/DNA / transcription regulator / TRANSCRIPTION-DNA complex
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
DNA / DNA (> 10) / Transcriptional regulator, TetR family protein
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 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 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator, TetR family
B: Transcriptional regulator, TetR family
C: Transcriptional regulator, TetR family
D: Transcriptional regulator, TetR family
E: DNA (31-MER)
F: DNA (31-MER)


Theoretical massNumber of molelcules
Total (without water)105,1106
Polymers105,1106
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14310 Å2
ΔGint-90 kcal/mol
Surface area38330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.954, 100.954, 99.856
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
Transcriptional regulator, TetR family / Transcriptional regulation / Transcriptional regulator / TetR family protein


Mass: 21511.529 Da / Num. of mol.: 4
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: DNA chain DNA (31-MER)


Mass: 9543.144 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (31-MER)


Mass: 9521.146 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.79 Å3/Da / Density % sol: 55.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 10% PEG3000, 100mM imidazole, 200mM lithium sulfate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 10, 2012
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 39254 / Num. obs: 39254 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 34.7
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.37 / Num. unique all: 1887 / % possible all: 95.1

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→35.497 Å / SU ML: 0.5 / σ(F): 1.96 / Phase error: 34.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2797 1948 5.02 %random
Rwork0.2241 ---
obs0.2241 38813 98.57 %-
all-39254 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.718 Å2 / ksol: 0.313 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--12.1068 Å2-0 Å20 Å2
2---12.1068 Å2-0 Å2
3---24.2137 Å2
Refinement stepCycle: LAST / Resolution: 2.5→35.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5506 1271 0 65 6842
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087014
X-RAY DIFFRACTIONf_angle_d1.3179754
X-RAY DIFFRACTIONf_dihedral_angle_d21.6552689
X-RAY DIFFRACTIONf_chiral_restr0.0831135
X-RAY DIFFRACTIONf_plane_restr0.0041046
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.56260.44761370.37292417X-RAY DIFFRACTION91
2.5626-2.63190.4451240.36732571X-RAY DIFFRACTION96
2.6319-2.70930.45571240.36022662X-RAY DIFFRACTION99
2.7093-2.79670.38711450.31772675X-RAY DIFFRACTION100
2.7967-2.89660.36161220.31632671X-RAY DIFFRACTION100
2.8966-3.01250.39021470.29562639X-RAY DIFFRACTION100
3.0125-3.14960.36561360.26232678X-RAY DIFFRACTION100
3.1496-3.31550.28621300.23152639X-RAY DIFFRACTION98
3.3155-3.52310.27971460.21942654X-RAY DIFFRACTION100
3.5231-3.79480.30611230.24632664X-RAY DIFFRACTION99
3.7948-4.17610.24981690.19372643X-RAY DIFFRACTION99
4.1761-4.77920.22281380.17122655X-RAY DIFFRACTION100
4.7792-6.01650.26751630.19622637X-RAY DIFFRACTION100
6.0165-35.50050.20661440.17662660X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -6.1555 Å / Origin y: -1.8485 Å / Origin z: -2.9845 Å
111213212223313233
T0.1926 Å20.0843 Å20.0046 Å2-0.1052 Å2-0.0111 Å2--0.1201 Å2
L0.8098 °20.7824 °2-0.4368 °2-0.8787 °2-0.3347 °2--0.607 °2
S0.0101 Å °0.0175 Å °-0.1349 Å °0.1151 Å °-0.0472 Å °-0.1295 Å °0.0516 Å °-0.0092 Å °0.0002 Å °
Refinement TLS groupSelection details: ALL

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