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- PDB-4nn1: Crystal Structure of transcriptional regulator Rv1219c of Mycobac... -

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Basic information

Entry
Database: PDB / ID: 4nn1
TitleCrystal Structure of transcriptional regulator Rv1219c of Mycobacterium tuberculosis
ComponentsTranscriptional regulatorTranscriptional regulation
KeywordsTRANSCRIPTION / Helix turn helix motif / DNA binding transcriptional regulator / DNA Binding
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
TetR transcriptional regulator Rv1219c-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
HTH-type transcriptional regulatory protein RaaS
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.99 Å
AuthorsKumar, N. / Radhakrishnan, A. / Chou, T.-H. / Yu, E.
CitationJournal: Protein Sci. / Year: 2014
Title: Crystal structure of the transcriptional regulator Rv1219c of Mycobacterium tuberculosis.
Authors: Kumar, N. / Radhakrishnan, A. / Wright, C.C. / Chou, T.H. / Lei, H.T. / Bolla, J.R. / Tringides, M.L. / Rajashankar, K.R. / Su, C.C. / Purdy, G.E. / Yu, E.W.
History
DepositionNov 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2May 7, 2014Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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


Theoretical massNumber of molelcules
Total (without water)24,0401
Polymers24,0401
Non-polymers00
Water0
1
A: Transcriptional regulator

A: Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)48,0812
Polymers48,0812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation38_775-y+5/2,-x+5/2,-z+1/21
Buried area6090 Å2
ΔGint-57 kcal/mol
Surface area20040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.876, 151.876, 151.876
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number211
Space group name H-MI432

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Components

#1: Protein Transcriptional regulator / Transcriptional regulation


Mass: 24040.256 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv1219c, RVBD_1219c / Plasmid: PET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O86312

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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: 3.04 Å3/Da / Density % sol: 59.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 5% Jeffamine M-600, 0.1M Na-citrate, 0.6M NaCl, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 29, 2013
RadiationMonochromator: cryogenically cooled silicon crystals (111-cuts)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.99→50 Å / Num. obs: 6216 / % possible obs: 98.6 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 2.7 % / Rmerge(I) obs: 0.06 / Χ2: 1.029 / Net I/σ(I): 13.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.99-3.182.70.45119050.979199.6
3.18-3.422.70.24218961.038199.6
3.42-3.772.70.12119231.088199.3
3.77-4.312.70.0818761.021199.2
4.31-5.432.80.05918880.985198
5.43-502.80.02618541.065195.7

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.1_1168refinement
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
SHELXSphasing
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.99→48.027 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.33 / σ(F): 1.35 / Phase error: 28.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2766 298 4.8 %RANDOM
Rwork0.2159 ---
all0.2187 6214 --
obs0.2187 6214 97.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.94 Å2 / Biso mean: 66.8602 Å2 / Biso min: 36.32 Å2
Refinement stepCycle: LAST / Resolution: 2.99→48.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1578 0 0 0 1578
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_deg1.191
X-RAY DIFFRACTIONf_bond_d0.009

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