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- PDB-3hth: Crystal structure of multidrug binding protein EbrR complexed wit... -

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Basic information

Entry
Database: PDB / ID: 3hth
TitleCrystal structure of multidrug binding protein EbrR complexed with proflavin
ComponentsEbrA repressor
KeywordsDNA BINDING PROTEIN / TetR Family / Multidrug resistance / Multidrug binding protein / DNA-binding / Transcription / Transcription regulation
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Tetracyclin repressor-like, C-terminal, group 31 / Tetracyclin repressor-like, C-terminal domain / 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
NICKEL (II) ION / PROFLAVIN / EbrA repressor
Similarity search - Component
Biological speciesStreptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsDong, J. / Ni, L. / Schumacher, M. / Brennan, R.
CitationJournal: To be Published
Title: Structural plasticity is key to multiple ligand binding by the multidrug binding regulator EbrR
Authors: Dong, J. / Ni, L. / Schumacher, M. / Brennan, R.
History
DepositionJun 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 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

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Assembly

Deposited unit
A: EbrA repressor
B: EbrA repressor
C: EbrA repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3938
Polymers69,7993
Non-polymers5955
Water1,45981
1
A: EbrA repressor
B: EbrA repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0686
Polymers46,5332
Non-polymers5364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-11.2 kcal/mol
Surface area15610 Å2
MethodPISA
2
C: EbrA repressor
hetero molecules

C: EbrA repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6504
Polymers46,5332
Non-polymers1172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area2690 Å2
ΔGint-12.4 kcal/mol
Surface area15200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.719, 99.719, 133.730
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-199-

NI

21C-200-

NI

31A-324-

HOH

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Components

#1: Protein EbrA repressor


Mass: 23266.268 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Strain: TK64 / Gene: ebrR / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q79SH7
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-PRL / PROFLAVIN / Proflavine


Mass: 209.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H11N3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.75 Å3/Da / Density % sol: 55.27 %
Crystal growTemperature: 295 K / pH: 8
Details: 1.4 M Lithium sulfate, 0.1 M Tris-HCl, 0.01 M Nickel chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 28, 2008
RadiationMonochromator: SI(111) DOUBLE FLAT CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→86.39 Å / Num. obs: 21657 / Redundancy: 5.8 % / Rmerge(I) obs: 0.064

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HTA

3hta


Resolution: 2.7→86.39 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2773 2151 9.9 %RANDOM
Rwork0.2276 ---
obs0.2276 21625 100 %-
Solvent computationBsol: 55.2274 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.891 Å20 Å20 Å2
2--9.891 Å20 Å2
3----19.782 Å2
Refinement stepCycle: LAST / Resolution: 2.7→86.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3896 0 35 81 4012
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.28
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_it1.3741.5
X-RAY DIFFRACTIONc_mcangle_it2.4172
X-RAY DIFFRACTIONc_scbond_it1.7522
X-RAY DIFFRACTIONc_scangle_it2.7992.5

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