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- PDB-3vvz: Crystal Strucuture of The Rhodamine 6G-Bound Form of RamR (Transc... -

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Basic information

Entry
Database: PDB / ID: 3vvz
TitleCrystal Strucuture of The Rhodamine 6G-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


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
RHODAMINE 6G / Putative regulatory protein / Putative regulatory protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.51 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)90,33612
Polymers88,1774
Non-polymers2,1588
Water68538
1
A: Putative regulatory protein
B: Putative regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1686
Polymers44,0892
Non-polymers1,0794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-53 kcal/mol
Surface area17850 Å2
MethodPISA
2
C: Putative regulatory protein
D: Putative regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1686
Polymers44,0892
Non-polymers1,0794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-53 kcal/mol
Surface area17440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.717, 54.329, 92.296
Angle α, β, γ (deg.)104.54, 97.32, 90.00
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-RHQ / RHODAMINE 6G


Mass: 443.557 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H31N2O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.39 Å3/Da / Density % sol: 48.45 % / Mosaicity: 1.004 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES, 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: Nov 27, 2010
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. obs: 27364 / % possible obs: 98.5 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.067 / Χ2: 1.869 / Net I/σ(I): 14.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.543.80.3714081.542198.4
2.54-2.593.80.31413461.687198.2
2.59-2.643.80.27813461.671198.2
2.64-2.693.80.24514211.463198.4
2.69-2.753.90.21613331.683198.7
2.75-2.823.90.17513561.24198.2
2.82-2.893.90.16614081.486199
2.89-2.963.90.13213171.289198.5
2.96-3.0540.12913831.497198.7
3.05-3.153.90.10413941.625198.9
3.15-3.263.90.08913421.617198.8
3.26-3.393.90.07813781.771198.9
3.39-3.553.80.06613781.959198.8
3.55-3.733.80.0613642.203199.3
3.73-3.973.70.05213962.202199.2
3.97-4.273.70.05113752.575199.3
4.27-4.713.70.04613732.638199.2
4.71-5.393.60.04614042.538199.4
5.39-6.793.60.04413612.504199.7
6.79-1003.40.03912812.6192.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.89 Å44.28 Å
Translation2.89 Å44.28 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: 2.51→44.28 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.859 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 16.072 / SU ML: 0.365 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.271 / ESU R Free: 0.375 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3014 1399 5.1 %RANDOM
Rwork0.2624 25890 --
obs0.2644 27289 97.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 110.01 Å2 / Biso mean: 53.4402 Å2 / Biso min: 18.76 Å2
Baniso -1Baniso -2Baniso -3
1-1.75 Å2-0.8 Å20.46 Å2
2---1.4 Å2-0.92 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 2.51→44.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5848 0 152 38 6038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0226112
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.9778252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.515732
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.39922.917288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.548151060
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3681560
X-RAY DIFFRACTIONr_chiral_restr0.10.2892
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024604
X-RAY DIFFRACTIONr_mcbond_it0.9741.53656
X-RAY DIFFRACTIONr_mcangle_it1.78425816
X-RAY DIFFRACTIONr_scbond_it2.38332456
X-RAY DIFFRACTIONr_scangle_it3.8464.52436
LS refinement shellResolution: 2.508→2.573 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 92 -
Rwork0.318 1777 -
all-1869 -
obs--87.87 %

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