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- PDB-6ie8: RamR in complex with cholic acid -

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Basic information

Entry
Database: PDB / ID: 6ie8
TitleRamR in complex with cholic acid
ComponentsRegulatory protein
KeywordsTRANSCRIPTION / transcriptional regulator / TetR Family
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
CHOLIC ACID / Putative regulatory protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsNakashima, R. / Sakurai, K. / Yamasaki, S. / Nishino, K.
CitationJournal: Sci Rep / Year: 2019
Title: Crystal structure of the multidrug resistance regulator RamR complexed with bile acids.
Authors: Yamasaki, S. / Nakashima, R. / Sakurai, K. / Baucheron, S. / Giraud, E. / Doublet, B. / Cloeckaert, A. / Nishino, K.
History
DepositionSep 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5493
Polymers22,0441
Non-polymers5052
Water41423
1
A: Regulatory protein
hetero molecules

A: Regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0986
Polymers44,0892
Non-polymers1,0094
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4510 Å2
ΔGint-43 kcal/mol
Surface area18150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.207, 53.613, 43.941
Angle α, β, γ (deg.)90.000, 93.220, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Regulatory protein


Mass: 22044.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain 14028s / SGSC 2262) (bacteria)
Strain: 14028s / SGSC 2262 / Gene: STM14_0676 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F6AY66
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CHD / CHOLIC ACID


Mass: 408.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H40O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.46 Å3/Da / Density % sol: 49.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1M MES pH6.5, 0.2M Ammonium Sulfate, 20% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 13733 / % possible obs: 99.1 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.068 / Χ2: 1.295 / Net I/av σ(I): 37.268 / Net I/σ(I): 11 / Num. measured all: 104226
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2-2.037.80.5216820.999199.1
2.03-2.077.70.4161.067198.7
2.07-2.117.70.3460.965199.3
2.11-2.157.80.3210.98198.8
2.15-2.27.60.2680.93199.1
2.2-2.257.70.241.104199.4
2.25-2.317.70.20.987199
2.31-2.377.70.1580.979199.4
2.37-2.447.70.1280.927199.2
2.44-2.527.70.1190.976199.4
2.52-2.617.70.1071.009199.6
2.61-2.717.70.0851.028199.4
2.71-2.847.70.0751.136199.9
2.84-2.997.70.0741.289199.6
2.99-3.177.60.0691.529199.7
3.17-3.427.50.061.967199.7
3.42-3.767.20.0562.281199.9
3.76-4.317.50.0442.181100
4.31-5.437.30.0371.991199.7
5.43-1006.80.0331.736194.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.18 Å43.87 Å
Translation2.18 Å43.87 Å

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
MOLREP10.2.35phasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VVX

3vvx


Resolution: 2→43.87 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.015 / SU ML: 0.114 / SU R Cruickshank DPI: 0.1816 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.163
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2321 687 5 %RANDOM
Rwork0.1878 ---
obs0.19 13046 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 146.91 Å2 / Biso mean: 43.997 Å2 / Biso min: 14.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 2→43.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1462 0 34 24 1520
Biso mean--39.35 40.03 -
Num. residues----184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191552
X-RAY DIFFRACTIONr_bond_other_d0.0010.021486
X-RAY DIFFRACTIONr_angle_refined_deg1.9981.9762105
X-RAY DIFFRACTIONr_angle_other_deg0.96233407
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7465189
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.35922.83874
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.19115270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8131516
X-RAY DIFFRACTIONr_chiral_restr0.1180.2238
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021737
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02371
LS refinement shellResolution: 1.997→2.049 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 60 -
Rwork0.229 927 -
all-987 -
obs--97.82 %

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