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- PDB-6a4l: AcrR from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 6a4l
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 / DNA binding
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 ...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 / SAD / Resolution: 2.8 Å
AuthorsKang, S.M.
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 20, 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 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)52,40210
Polymers51,8532
Non-polymers5498
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-139 kcal/mol
Surface area18650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.752, 118.752, 93.456
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: 25926.330 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.67 Å3/Da / Density % sol: 69.7 %
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: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 18576 / % possible obs: 100 % / Redundancy: 31.3 % / Rpim(I) all: 0.017 / Net I/σ(I): 45.3
Reflection shellResolution: 2.8→2.85 Å / Num. unique obs: 930 / Rpim(I) all: 0.118

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→45.052 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.81
RfactorNum. reflection% reflection
Rfree0.2585 1851 5.13 %
Rwork0.2127 --
obs0.215 18493 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→45.052 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3090 0 28 93 3211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063172
X-RAY DIFFRACTIONf_angle_d1.3444307
X-RAY DIFFRACTIONf_dihedral_angle_d14.6471171
X-RAY DIFFRACTIONf_chiral_restr0.043485
X-RAY DIFFRACTIONf_plane_restr0.005560
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7993-2.8750.37121270.28042642X-RAY DIFFRACTION99
2.875-2.95950.3621530.24332649X-RAY DIFFRACTION100
2.9595-3.0550.26131420.23332633X-RAY DIFFRACTION100
3.055-3.16420.31671510.23742636X-RAY DIFFRACTION100
3.1642-3.29090.34281620.23912631X-RAY DIFFRACTION100
3.2909-3.44060.2951570.24232646X-RAY DIFFRACTION100
3.4406-3.62190.30011330.22182583X-RAY DIFFRACTION97
3.6219-3.84870.22681340.2182587X-RAY DIFFRACTION98
3.8487-4.14570.22851690.20222620X-RAY DIFFRACTION100
4.1457-4.56250.21071570.17332671X-RAY DIFFRACTION100
4.5625-5.22190.19851400.17862639X-RAY DIFFRACTION100
5.2219-6.57580.2741160.24452680X-RAY DIFFRACTION100
6.5758-45.05770.21581100.182649X-RAY DIFFRACTION99

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