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- PDB-6a4w: AcrR from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 6a4w
TitleAcrR from Mycobacterium tuberculosis
ComponentsTetR family transcriptional regulator
KeywordsTRANSCRIPTION / Transcription regulator
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
BetI-type transcriptional repressor, C-terminal / BetI-type transcriptional repressor, C-terminal / 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 regulator AcrR / Probable transcriptional regulatory protein (Probably TetR/AcrR-family)
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.587 Å
AuthorsKang, S.M. / Kim, D.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)2018R1A2A1A19018526 Korea, Republic Of
CitationJournal: Febs Open Bio / Year: 2019
Title: The crystal structure of AcrR from Mycobacterium tuberculosis reveals a one-component transcriptional regulation mechanism.
Authors: Kang, S.M. / Kim, D.H. / Jin, C. / Ahn, H.C. / Lee, B.J.
History
DepositionJun 21, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Structure summary / Category: citation / citation_author / struct
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 / _struct.title
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TetR family transcriptional regulator
B: TetR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5498
Polymers51,1962
Non-polymers3536
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-90 kcal/mol
Surface area18720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.154, 118.154, 90.906
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein TetR family transcriptional regulator


Mass: 25598.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: acrR, ERS007657_03305, ERS007663_01106, ERS007670_02655, ERS007672_02023, ERS007679_02277, ERS007681_02293, ERS007688_01622, ERS007703_02625, ERS007722_01260, ERS023446_03575, ERS027646_00827, ...Gene: acrR, ERS007657_03305, ERS007663_01106, ERS007670_02655, ERS007672_02023, ERS007679_02277, ERS007681_02293, ERS007688_01622, ERS007703_02625, ERS007722_01260, ERS023446_03575, ERS027646_00827, ERS027651_03158, ERS027653_04028, ERS027654_02941, ERS027659_02538, ERS027661_02360, ERS031537_01877, ERS124361_02153, SAMEA2682864_00974, SAMEA2683035_01767
Production host: Escherichia coli (E. coli) / References: UniProt: A0A045J2D2, UniProt: O07229*PLUS
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Na
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 3.58 Å3/Da / Density % sol: 69.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1260 mM Ammonium sulfate 100 mM MES/ Sodium hydroxide pH 6.0

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.587→50 Å / Num. obs: 21205 / % possible obs: 94.3 % / Redundancy: 5.9 % / Rpim(I) all: 0.053 / Net I/σ(I): 28.7
Reflection shellResolution: 2.6→2.64 Å / Num. unique obs: 1086 / Rpim(I) all: 0.282

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A4L

6a4l


Resolution: 2.587→49.536 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.03
RfactorNum. reflection% reflection
Rfree0.2489 1085 5.12 %
Rwork0.1997 --
obs0.2021 21184 93.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.587→49.536 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3100 0 19 67 3186
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063165
X-RAY DIFFRACTIONf_angle_d1.3314290
X-RAY DIFFRACTIONf_dihedral_angle_d14.9631176
X-RAY DIFFRACTIONf_chiral_restr0.04484
X-RAY DIFFRACTIONf_plane_restr0.004559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5869-2.70460.28071380.23922424X-RAY DIFFRACTION91
2.7046-2.84720.27451510.23382557X-RAY DIFFRACTION96
2.8472-3.02550.34281150.23682594X-RAY DIFFRACTION96
3.0255-3.25910.27651350.23172563X-RAY DIFFRACTION96
3.2591-3.5870.27521540.22172524X-RAY DIFFRACTION95
3.587-4.10580.23871410.19222508X-RAY DIFFRACTION94
4.1058-5.1720.22361340.17112440X-RAY DIFFRACTION91
5.172-49.54480.20441170.17682489X-RAY DIFFRACTION90

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