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

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Basic information

Entry
Database: PDB / ID: 3hta
TitleCrystal structure of multidrug binding protein EbrR complexed with imidazole
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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
IMIDAZOLE / EbrA repressor
Similarity search - Component
Biological speciesStreptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)93,3418
Polymers93,0654
Non-polymers2764
Water3,027168
1
A: EbrA repressor
B: EbrA repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6714
Polymers46,5332
Non-polymers1382
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-14.6 kcal/mol
Surface area17190 Å2
MethodPISA
2
C: EbrA repressor
D: EbrA repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6714
Polymers46,5332
Non-polymers1382
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-11.9 kcal/mol
Surface area16960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.471, 77.922, 203.265
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
EbrA repressor


Mass: 23266.268 Da / Num. of mol.: 4
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-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 3.25 Å3/Da / Density % sol: 62.2 %
Crystal growTemperature: 295 K / pH: 7
Details: 30% PEG 1000, 0.1 M Calcium chloride, 0.1 M Imidazole, pH 7.0, 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: 1.02003
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 9, 2007
RadiationMonochromator: SI(111) DOUBLE FLAT CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02003 Å / Relative weight: 1
ReflectionResolution: 2.3→67.7 Å / Num. obs: 54199 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 48.3

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Processing

Software
NameVersionClassification
PHASERphasing
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MODEL FORM MAD DATA OF EBRR

Resolution: 2.3→67.7 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2922 2160 5 %RANDOM
Rwork0.2524 ---
obs0.2524 42351 98.7 %-
all-54199 --
Solvent computationBsol: 42.0185 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.779 Å20 Å20 Å2
2--24.405 Å20 Å2
3----21.626 Å2
Refinement stepCycle: LAST / Resolution: 2.3→67.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5581 0 20 168 5769
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_it1.1681.5
X-RAY DIFFRACTIONc_mcangle_it1.9262
X-RAY DIFFRACTIONc_scbond_it1.9662
X-RAY DIFFRACTIONc_scangle_it2.882.5

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