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- PDB-3vw2: Crystal Strucuture of The Berberine-bound Form of RamR (Transcrip... -

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Basic information

Entry
Database: PDB / ID: 3vw2
TitleCrystal Strucuture of The Berberine-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
BERBERINE / Putative regulatory protein / Putative regulatory protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.34 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)89,90712
Polymers88,1774
Non-polymers1,7308
Water1,20767
1
A: Putative regulatory protein
B: Putative regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9536
Polymers44,0892
Non-polymers8654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-47 kcal/mol
Surface area17980 Å2
MethodPISA
2
C: Putative regulatory protein
D: Putative regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9536
Polymers44,0892
Non-polymers8654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-49 kcal/mol
Surface area17770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.817, 54.623, 92.291
Angle α, β, γ (deg.)104.970, 97.740, 90.040
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-BER / BERBERINE


Mass: 336.361 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H18NO4
#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.: 67 / 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: 2.4 Å3/Da / Density % sol: 48.67 % / Mosaicity: 1.037 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES, 20mM NaPi, 75mM NaCl, 0.2M Ammonium sulfate, 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: Jan 23, 2012
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.34→50 Å / Num. obs: 32813 / % possible obs: 95.1 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.075 / Χ2: 1.911 / Net I/σ(I): 11.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.35-2.393.60.4115451.266190.9
2.39-2.433.50.36916431.301192.5
2.43-2.483.60.33815491.331191.6
2.48-2.533.50.3316091.357193.3
2.53-2.593.50.27816101.422191.6
2.59-2.653.50.25115731.501193.1
2.65-2.713.40.23416231.637193.1
2.71-2.793.40.19116071.737194.5
2.79-2.873.30.18316561.807194.8
2.87-2.963.20.15416561.93196
2.96-3.073.20.14216851.958197.5
3.07-3.193.10.11516852.156197.5
3.19-3.333.10.09216802.138197.7
3.33-3.5130.08117022.311198.7
3.51-3.7330.06317152.394198.6
3.73-4.022.90.05716802.526198.5
4.02-4.422.90.05217222.615198.9
4.42-5.062.90.04716892.607198.6
5.06-6.372.90.0517182.544199.2
6.37-502.70.04314662.624185

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.62 Å43.39 Å
Translation2.62 Å43.39 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: 2.34→41.29 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.909 / WRfactor Rfree: 0.2634 / WRfactor Rwork: 0.2313 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8115 / SU B: 7.16 / SU ML: 0.176 / SU R Cruickshank DPI: 0.5095 / SU Rfree: 0.2789 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.509 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1693 5.2 %RANDOM
Rwork0.2248 ---
obs0.2266 32793 94.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 112.53 Å2 / Biso mean: 53.5272 Å2 / Biso min: 16.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20.02 Å2-0.03 Å2
2--0.09 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.34→41.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5845 0 120 67 6032
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0226085
X-RAY DIFFRACTIONr_angle_refined_deg1.7461.9758224
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3755732
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.5222.892287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.956151059
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8481560
X-RAY DIFFRACTIONr_chiral_restr0.1340.2900
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024580
X-RAY DIFFRACTIONr_mcbond_it1.5121.53660
X-RAY DIFFRACTIONr_mcangle_it2.69925824
X-RAY DIFFRACTIONr_scbond_it3.59632425
X-RAY DIFFRACTIONr_scangle_it5.4244.52400
LS refinement shellResolution: 2.337→2.398 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 100 -
Rwork0.281 2075 -
all-2175 -
obs--85.16 %

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