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- PDB-3vw0: Crystal Structure of The Dequalinum-bound Form of RamR (Transcrip... -

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Basic information

Entry
Database: PDB / ID: 3vw0
TitleCrystal Structure of The Dequalinum-bound Form of RamR (Transcriptional Regulator 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
DEQUALINIUM / Putative regulatory protein / Putative regulatory protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSakurai, K. / Yamasaki, S. / Nakashima, R. / Nikaido, E. / 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)89,47510
Polymers88,1774
Non-polymers1,2986
Water97354
1
A: Putative regulatory protein
B: Putative regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7375
Polymers44,0892
Non-polymers6493
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-52 kcal/mol
Surface area18510 Å2
MethodPISA
2
C: Putative regulatory protein
D: Putative regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7375
Polymers44,0892
Non-polymers6493
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-54 kcal/mol
Surface area18590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.345, 43.551, 106.692
Angle α, β, γ (deg.)90.000, 100.210, 90.000
Int Tables number5
Space group name H-MC121

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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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DEQ / DEQUALINIUM / DEQUADIN


Mass: 456.665 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H40N4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.43 Å3/Da / Density % sol: 49.36 % / Mosaicity: 0.357 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.67
Details: 0.1M MES, 20mM NaPi, 75mM NaCl, 0.2M Ammonium sulfate, 2mM DTT, 25% PEG 6000, pH 6.67, 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 23, 2011
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 26448 / % possible obs: 99.8 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.072 / Χ2: 1.356 / Net I/σ(I): 11.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.6-2.647.60.45812911.0251100
2.64-2.697.50.39813151.0481100
2.69-2.747.60.3513200.9841100
2.74-2.87.60.31212911.0011100
2.8-2.867.60.26313300.9781100
2.86-2.937.60.22513081.0031100
2.93-37.60.19912930.9641100
3-3.087.60.16113380.9721100
3.08-3.177.60.13412800.9691100
3.17-3.287.60.10613380.9831100
3.28-3.397.60.09213141.0731100
3.39-3.537.60.07913041.1321100
3.53-3.697.60.06613491.3621100
3.69-3.887.50.06713081.7481100
3.88-4.137.40.06213252.151100
4.13-4.457.10.05613342.4241100
4.45-4.897.20.05313262.4931100
4.89-5.67.40.0513441.8331100
5.6-7.057.30.03813621.5471100
7.05-506.50.02913781.581196.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→38.15 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.907 / WRfactor Rfree: 0.2625 / WRfactor Rwork: 0.221 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8081 / SU B: 10.417 / SU ML: 0.226 / SU R Cruickshank DPI: 1.4699 / SU Rfree: 0.3472 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.47 / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2668 1334 5.1 %RANDOM
Rwork0.2241 ---
obs0.2263 26359 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 173.05 Å2 / Biso mean: 50.6341 Å2 / Biso min: 10 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20.04 Å2
2---0.1 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.6→38.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5851 0 88 54 5993
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0226049
X-RAY DIFFRACTIONr_angle_refined_deg1.571.9668160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5125733
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.43522.892287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.905151060
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1041560
X-RAY DIFFRACTIONr_chiral_restr0.1020.2893
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024548
X-RAY DIFFRACTIONr_mcbond_it1.2271.53665
X-RAY DIFFRACTIONr_mcangle_it2.34725832
X-RAY DIFFRACTIONr_scbond_it3.2632384
X-RAY DIFFRACTIONr_scangle_it5.3874.52328
LS refinement shellResolution: 2.604→2.671 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 84 -
Rwork0.296 1785 -
all-1869 -
obs--96.89 %

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