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- PDB-5ydd: Crystal structure of C-terminal domain of Rv1828 from Mycobacteri... -

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Basic information

Entry
Database: PDB / ID: 5ydd
TitleCrystal structure of C-terminal domain of Rv1828 from Mycobacterium tuberculosis
ComponentsUncharacterized HTH-type transcriptional regulator Rv1828
KeywordsTRANSCRIPTION REGULATOR / DNA binding / HTH motif / promoter / dimer
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / cytosol
Similarity search - Function
: / MerR HTH family regulatory protein / helix_turn_helix, mercury resistance / MerR-type HTH domain profile. / MerR-type HTH domain / Putative DNA-binding domain superfamily
Similarity search - Domain/homology
Chem-8TU / Uncharacterized HTH-type transcriptional regulator Rv1828
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSingh, S. / Karthiekeyan, S.
Funding support India, 1items
OrganizationGrant numberCountry
CSIR-Institute of Microbial TechnologyBSC0210 India
CitationJournal: FEBS J. / Year: 2018
Title: Characteristics of the essential pathogenicity factor Rv1828, a MerR family transcription regulator from Mycobacterium tuberculosis.
Authors: Singh, S. / Sevalkar, R.R. / Sarkar, D. / Karthikeyan, S.
History
DepositionSep 12, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 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

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Assembly

Deposited unit
A: Uncharacterized HTH-type transcriptional regulator Rv1828
B: Uncharacterized HTH-type transcriptional regulator Rv1828
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6156
Polymers31,0832
Non-polymers5324
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-76 kcal/mol
Surface area12410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.035, 31.452, 76.998
Angle α, β, γ (deg.)90.00, 97.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Uncharacterized HTH-type transcriptional regulator Rv1828


Mass: 15541.634 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 127-247
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: Rv1828, MTCY1A11.15c / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P9WME7

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Non-polymers , 5 types, 194 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-8TU / (6R,8S,9S)-8-(hydroxymethyl)-6,11,11-tris(oxidanyl)-9-propyl-dodecanoic acid


Mass: 320.422 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O6
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 2.2 M Ammonium sulfate, 0.1 M Bis-Tris (pH 6.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 33255 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.02 / Net I/σ(I): 23.3
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.6 / % possible all: 93.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YDC

5ydc


Resolution: 1.5→27.24 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.342 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.083 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.209 1671 5 %RANDOM
Rwork0.154 ---
obs0.157 31581 96.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å2-1.53 Å2
2---1.78 Å20 Å2
3---1.29 Å2
Refinement stepCycle: LAST / Resolution: 1.5→27.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1780 0 34 190 2004
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191887
X-RAY DIFFRACTIONr_bond_other_d0.0030.021880
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.9992562
X-RAY DIFFRACTIONr_angle_other_deg1.0143.0054323
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4455254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06522.77872
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70315322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7471519
X-RAY DIFFRACTIONr_chiral_restr0.0950.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022119
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02372
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2111.776993
X-RAY DIFFRACTIONr_mcbond_other2.1471.772992
X-RAY DIFFRACTIONr_mcangle_it2.6962.6771248
X-RAY DIFFRACTIONr_mcangle_other2.6952.6821249
X-RAY DIFFRACTIONr_scbond_it3.1572.272894
X-RAY DIFFRACTIONr_scbond_other3.1532.272894
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5733.2571312
X-RAY DIFFRACTIONr_long_range_B_refined4.94524.4552168
X-RAY DIFFRACTIONr_long_range_B_other4.94424.4712169
X-RAY DIFFRACTIONr_rigid_bond_restr2.30833767
X-RAY DIFFRACTIONr_sphericity_free42.3715105
X-RAY DIFFRACTIONr_sphericity_bonded17.14953830
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 115 -
Rwork0.227 2219 -
obs--92.44 %

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