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- PDB-1r8d: Crystal Structure of MtaN Bound to DNA -

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Basic information

Entry
Database: PDB / ID: 1r8d
TitleCrystal Structure of MtaN Bound to DNA
Components
  • (26-MER) x 2
  • transcription activator MtaN
KeywordsTranscription/DNA / protein-DNA complex / Transcription-DNA COMPLEX
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / cytoplasm
Similarity search - Function
TipA-like multidrug resistance regulator, antibiotic-recognition domain / TipAS antibiotic-recognition domain / TipAS antibiotic-recognition domain / MerR, DNA binding / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 - #10 / MerR family regulatory protein / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 / : / MerR HTH family regulatory protein / MerR-type HTH domain profile. ...TipA-like multidrug resistance regulator, antibiotic-recognition domain / TipAS antibiotic-recognition domain / TipAS antibiotic-recognition domain / MerR, DNA binding / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 - #10 / MerR family regulatory protein / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 / : / MerR HTH family regulatory protein / MerR-type HTH domain profile. / helix_turn_helix, mercury resistance / MerR-type HTH domain / Putative DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / HTH-type transcriptional activator mta
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.7 Å
AuthorsNewberry, K.J. / Brennan, R.G.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: The structural mechanism for transcription activation by MerR family member multidrug transporter activation, N terminus.
Authors: Newberry, K.J. / Brennan, R.G.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: Crystal structure of MtaN, a global multidrug transporter gene activator
Authors: Godsey, M.H. / Baranova, N.N. / Neyfakh, A.A. / Brennan, R.G.
History
DepositionOct 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
C: 26-MER
D: 26-MER
A: transcription activator MtaN
B: transcription activator MtaN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8896
Polymers41,6974
Non-polymers1922
Water64936
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.190, 148.190, 73.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: DNA chain 26-MER


Mass: 7975.135 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 26-MER


Mass: 7998.209 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein transcription activator MtaN


Mass: 12861.807 Da / Num. of mol.: 2 / Fragment: N-terminal truncation mutant of mta
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: mta / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / References: UniProt: P71039
#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.: 36 / 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: 4.76 Å3/Da / Density % sol: 74.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 1450, lithium sulfate, PIPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 145011
2lithium sulfate11
3PIPES11
4H2O11
5PEG 145012
6lithium sulfate12
7H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 14, 2003
RadiationMonochromator: single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→35.8 Å / Num. all: 21954 / Num. obs: 21769 / % possible obs: 99 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 7.5 % / Biso Wilson estimate: 73.7 Å2 / Net I/σ(I): 22.2
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 3136 / % possible all: 98.6

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 2.7→19.75 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 2161 9.9 %RANDOM
Rwork0.234 ---
obs0.234 21733 98.9 %-
all-21954 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.0408 Å2 / ksol: 0.297524 e/Å3
Displacement parametersBiso mean: 65.4 Å2
Baniso -1Baniso -2Baniso -3
1-11.83 Å20 Å20 Å2
2--11.83 Å20 Å2
3----23.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.7→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1752 1060 10 36 2858
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d19.6
X-RAY DIFFRACTIONc_improper_angle_d1.16
X-RAY DIFFRACTIONc_mcbond_it5.781.5
X-RAY DIFFRACTIONc_mcangle_it8.22
X-RAY DIFFRACTIONc_scbond_it10.292
X-RAY DIFFRACTIONc_scangle_it12.942.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.472 349 9.8 %
Rwork0.4 3206 -
obs--98.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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