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

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Basic information

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


transcription cis-regulatory region binding / DNA-binding transcription factor activity
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 ...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
MALACHITE GREEN / EbrA repressor
Similarity search - Component
Biological speciesStreptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5962
Polymers23,2661
Non-polymers3291
Water37821
1
A: EbrA repressor
hetero molecules

A: EbrA repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1914
Polymers46,5332
Non-polymers6592
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area2780 Å2
ΔGint-14.2 kcal/mol
Surface area16280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.910, 59.910, 110.236
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein EbrA repressor


Mass: 23266.268 Da / Num. of mol.: 1
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-MGR / MALACHITE GREEN


Mass: 329.458 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H25N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.45 Å3/Da / Density % sol: 49.89 %
Crystal growTemperature: 295 K / pH: 6.8
Details: 50% Tacsimate, 0.1 M Magnesium sulfate, 0.1 M Cacodylate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Sep 21, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.5→30.06 Å / Num. obs: 8937 / Redundancy: 4.4 % / Rmerge(I) obs: 0.031

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
CNS1.1refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HTA

3hta


Resolution: 2.5→30.06 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2864 493 5.2 %RANDOM
Rwork0.2535 ---
obs0.2535 8937 95 %-
Solvent computationBsol: 55.1415 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.142 Å20 Å20 Å2
2---2.142 Å20 Å2
3---4.284 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1310 0 25 21 1356
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.26
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_it1.4041.5
X-RAY DIFFRACTIONc_mcangle_it2.4492
X-RAY DIFFRACTIONc_scbond_it1.7822
X-RAY DIFFRACTIONc_scangle_it2.6952.5

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