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- PDB-4kdp: TcaR-ssDNA complex crystal structure reveals the novel ssDNA bind... -

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Basic information

Entry
Database: PDB / ID: 4kdp
TitleTcaR-ssDNA complex crystal structure reveals the novel ssDNA binding mechanism of the MarR family proteins
Components
  • DNA (5'-D(*CP*GP*CP*AP*GP*CP*GP*CP*GP*CP*AP*GP*CP*CP*CP*TP*A)-3')
  • TcaR transcription regulator
KeywordsTRANSCRIPTION/DNA / Multiple drug resistance / ssDNA binding / antibiotics / Staphylococci / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
MarR family / ArsR-like helix-turn-helix domain / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / TcaR transcription regulator / TcaR transcription regulator
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsChang, Y.M. / Chen, C.K.-M. / Wang, A.H.-J.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: TcaR-ssDNA complex crystal structure reveals new DNA binding mechanism of the MarR family proteins.
Authors: Chang, Y.M. / Ho, C.H. / Chen, C.K. / Maestre-Reyna, M. / Chang-Chien, M.W. / Wang, A.H.
History
DepositionApr 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2Sep 20, 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_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
A: TcaR transcription regulator
B: TcaR transcription regulator
C: TcaR transcription regulator
D: TcaR transcription regulator
E: TcaR transcription regulator
F: TcaR transcription regulator
G: TcaR transcription regulator
H: DNA (5'-D(*CP*GP*CP*AP*GP*CP*GP*CP*GP*CP*AP*GP*CP*CP*CP*TP*A)-3')
J: DNA (5'-D(*CP*GP*CP*AP*GP*CP*GP*CP*GP*CP*AP*GP*CP*CP*CP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,94720
Polymers131,9649
Non-polymers98311
Water1,63991
1
A: TcaR transcription regulator
B: TcaR transcription regulator
H: DNA (5'-D(*CP*GP*CP*AP*GP*CP*GP*CP*GP*CP*AP*GP*CP*CP*CP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4079
Polymers39,9153
Non-polymers4936
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: TcaR transcription regulator
D: TcaR transcription regulator
J: DNA (5'-D(*CP*GP*CP*AP*GP*CP*GP*CP*GP*CP*AP*GP*CP*CP*CP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1595
Polymers39,9153
Non-polymers2442
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: TcaR transcription regulator
F: TcaR transcription regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0035
Polymers34,7562
Non-polymers2463
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: TcaR transcription regulator

G: TcaR transcription regulator


Theoretical massNumber of molelcules
Total (without water)34,7562
Polymers34,7562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465y-1,x+1,-z1
Unit cell
Length a, b, c (Å)91.899, 91.899, 261.534
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
TcaR transcription regulator


Mass: 17378.195 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis (bacteria) / Strain: ATCC 12228 / Gene: SE_1937 / Plasmid: pET32 Xa/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8CN94, UniProt: A0A0H2VJZ8*PLUS
#2: DNA chain DNA (5'-D(*CP*GP*CP*AP*GP*CP*GP*CP*GP*CP*AP*GP*CP*CP*CP*TP*A)-3')


Mass: 5158.339 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 40 % ethylene glycol, 0.1 M Tris , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Jan 28, 2012 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→30 Å / Num. all: 15185 / Num. obs: 15179 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 18.2
Reflection shellResolution: 3.6→3.73 Å / Redundancy: 3 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 2.1 / % possible all: 99.7

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KP7

3kp7


Resolution: 3.6→16 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.285 706 RANDOM
Rwork0.274 --
obs0.274 14084 -
Displacement parametersBiso mean: 112.238 Å2
Refinement stepCycle: LAST / Resolution: 3.6→16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8509 420 64 91 9084
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.985
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.6→3.73 Å
RfactorNum. reflection% reflection
Rfree0.438 57 -
Rwork0.373 --
obs--84.12 %

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