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- PDB-3lhq: DNA-binding transcriptional repressor AcrR from Salmonella typhim... -

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Basic information

Entry
Database: PDB / ID: 3lhq
TitleDNA-binding transcriptional repressor AcrR from Salmonella typhimurium.
ComponentsAcrAB operon repressor (TetR/AcrR family)
KeywordsTRANSCRIPTION / structural genomics / IDP02616 / CSGID / DNA-binding / repressor / AcrR / Transcription regulation / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
Transcription regulator MAATS, C-terminal / MAATS-type transcriptional repressor, C-terminal region / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / 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. ...Transcription regulator MAATS, C-terminal / MAATS-type transcriptional repressor, C-terminal region / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / 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
DI(HYDROXYETHYL)ETHER / AcrAB operon repressor (TetR/AcrR family)
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsOsipiuk, J. / Mulligan, R. / Papazisi, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: X-ray crystal structure of DNA-binding transcriptional repressor AcrR from Salmonella typhimurium.
Authors: Osipiuk, J. / Mulligan, R. / Papazisi, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AcrAB operon repressor (TetR/AcrR family)
B: AcrAB operon repressor (TetR/AcrR family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6855
Polymers50,4102
Non-polymers2743
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-25 kcal/mol
Surface area19110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.180, 75.820, 55.176
Angle α, β, γ (deg.)90.000, 108.670, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein AcrAB operon repressor (TetR/AcrR family)


Mass: 25205.127 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: acrR, STM0477 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7CR15
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 1.85 Å3/Da / Density % sol: 33.68 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M sodium chloride, 0.1 M Bis-Tris buffer, 25% PEG-3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 21, 2009
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: 1.56→37.9 Å / Num. all: 51039 / Num. obs: 51039 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.054 / Χ2: 1.141 / Net I/σ(I): 9.3
Reflection shellResolution: 1.56→1.59 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.759 / Mean I/σ(I) obs: 2.12 / Num. unique all: 2219 / Χ2: 1.319 / % possible all: 85.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QOP

2qop


Resolution: 1.56→37.9 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 3.627 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.134 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.199 2597 5.1 %RANDOM
Rwork0.15 ---
all0.153 50990 --
obs0.153 50990 97.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 78.8 Å2 / Biso mean: 19.813 Å2 / Biso min: 6.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å2-0.04 Å2
2--0.2 Å20 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.56→37.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3652 0 18 281 3951
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223769
X-RAY DIFFRACTIONr_bond_other_d0.0010.022682
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.9725134
X-RAY DIFFRACTIONr_angle_other_deg1.0136564
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9655499
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.50823.424184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.20715751
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3361538
X-RAY DIFFRACTIONr_chiral_restr0.1010.2585
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024189
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02791
X-RAY DIFFRACTIONr_mcbond_it1.81.52239
X-RAY DIFFRACTIONr_mcbond_other0.6241.5888
X-RAY DIFFRACTIONr_mcangle_it2.80223663
X-RAY DIFFRACTIONr_scbond_it4.57431530
X-RAY DIFFRACTIONr_scangle_it6.74.51431
X-RAY DIFFRACTIONr_rigid_bond_restr1.86236451
LS refinement shellResolution: 1.561→1.601 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 165 -
Rwork0.264 3207 -
all-3372 -
obs-3372 88 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1285-0.0729-0.20970.08550.12450.75520.02470.01160.0221-0.02690.0080.019-0.0033-0.0382-0.03270.0137-0.0064-0.00320.01140.00930.02850.607226.785933.7451
20.12880.0424-0.17620.1716-0.21310.67610.0047-0.02870.007-0.02510.0076-0.00350.02320.0831-0.01230.0139-0.00150.00060.0221-0.00310.002621.165437.972541.3547
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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