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- PDB-3vvy: Crystal Strucuture of The Ethidium-Bound Form of RamR (Transcript... -

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Basic information

Entry
Database: PDB / ID: 3vvy
TitleCrystal Strucuture of The Ethidium-Bound Form of RamR (Transcriptional Regurator of TetR Family) from Salmonella Typhimurium
ComponentsPutative regulatory protein
KeywordsTRANSCRIPTION REGULATOR / TetR transcriptional regulator family / HTH-Motif / Transcriptional regulator / DNA Binding
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / DNA binding
Similarity search - Function
DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Tetracycline Repressor, domain 2 / 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
ETHIDIUM / Putative regulatory protein / Putative regulatory protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.63 Å
AuthorsSakurai, K. / Nikaido, E. / Nakashima, R. / Yamasaki, S. / Yamaguchi, A. / Nishino, K.
CitationJournal: Nat Commun / Year: 2013
Title: The crystal structure of multidrug-resistance regulator RamR with multiple drugs
Authors: Yamasaki, S. / Nikaido, E. / Nakashima, R. / Sakurai, K. / Fujiwara, D. / Fujii, I. / Nishino, K.
History
DepositionJul 30, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Mar 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative regulatory protein
B: Putative regulatory protein
C: Putative regulatory protein
D: Putative regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4358
Polymers88,1774
Non-polymers1,2584
Water7,206400
1
A: Putative regulatory protein
B: Putative regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7174
Polymers44,0892
Non-polymers6292
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-23 kcal/mol
Surface area17840 Å2
MethodPISA
2
C: Putative regulatory protein
D: Putative regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7174
Polymers44,0892
Non-polymers6292
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-20 kcal/mol
Surface area17590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.398, 54.282, 91.864
Angle α, β, γ (deg.)103.840, 98.280, 89.970
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Putative regulatory protein / RamR / TetR-like transcriptional regulator


Mass: 22044.262 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: 14028s / Gene: STM0580, STM14_0676 / Plasmid: pET Duet / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: D0ZP76, UniProt: A0A0F6AY66*PLUS
#2: Chemical
ChemComp-ET / ETHIDIUM


Mass: 314.404 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H20N3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 2.41 Å3/Da / Density % sol: 48.98 % / Mosaicity: 0.237 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Sodium citrate, 20mM NaPi, 0.2M Ammonium sulfate, 75mM NaCl, 2mM DTT, 20% PEG 6000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 24, 2010
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. obs: 99066 / % possible obs: 97 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.047 / Χ2: 1.533 / Net I/σ(I): 15
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.63-1.662.90.3447731.139194.3
1.66-1.693.10.31249311.257196
1.69-1.723.20.28848841.212195.9
1.72-1.763.30.26149501.238196.7
1.76-1.793.40.23949731.338196.6
1.79-1.843.50.22548761.346196.7
1.84-1.883.60.20649681.552197.3
1.88-1.933.70.20149961.931196.4
1.93-1.993.80.16849511.698197.9
1.99-2.053.90.14349611.729197.3
2.05-2.1340.11949971.637197.4
2.13-2.2140.09649751.641197.8
2.21-2.3140.0850291.588198.2
2.31-2.4340.06349961.567198.1
2.43-2.5940.05650371.487198.3
2.59-2.7940.04850041.527198.4
2.79-3.0740.04150511.59199
3.07-3.513.90.03650581.734198.9
3.51-4.423.80.03150041.711197.9
4.42-503.70.02546521.287191.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.95 Å41.86 Å
Translation1.95 Å41.86 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→41.86 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.2358 / WRfactor Rwork: 0.1985 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8508 / SU B: 1.782 / SU ML: 0.062 / SU R Cruickshank DPI: 0.0991 / SU Rfree: 0.1006 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2278 4935 5 %RANDOM
Rwork0.1909 ---
obs0.1927 98895 96.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 75.03 Å2 / Biso mean: 29.455 Å2 / Biso min: 9.3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.63→41.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5854 0 96 400 6350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0226215
X-RAY DIFFRACTIONr_angle_refined_deg2.3041.9698415
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2825777
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57222.755294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.101151110
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6831564
X-RAY DIFFRACTIONr_chiral_restr0.1590.2915
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.024722
X-RAY DIFFRACTIONr_mcbond_it1.551.53742
X-RAY DIFFRACTIONr_mcangle_it2.7125981
X-RAY DIFFRACTIONr_scbond_it4.28632473
X-RAY DIFFRACTIONr_scangle_it7.0064.52417
LS refinement shellResolution: 1.633→1.675 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 343 -
Rwork0.251 6624 -
all-6967 -
obs--92.38 %

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