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- PDB-6ie9: RamR in complex with chenodeoxycholic acid -

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Basic information

Entry
Database: PDB / ID: 6ie9
TitleRamR in complex with chenodeoxycholic 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
CHENODEOXYCHOLIC ACID / Putative regulatory protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.78 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)22,5333
Polymers22,0441
Non-polymers4892
Water63135
1
A: Regulatory protein
hetero molecules

A: Regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0666
Polymers44,0892
Non-polymers9774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2470 Å2
ΔGint-17 kcal/mol
Surface area18430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.436, 53.576, 43.837
Angle α, β, γ (deg.)90.000, 93.290, 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-JN3 / CHENODEOXYCHOLIC ACID / (3ALPHA,5ALPHA,7BETA,8ALPHA,17ALPHA)-3,7-DIHYDROXYCHOLAN-24-OIC ACID


Mass: 392.572 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H40O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.45 Å3/Da / Density % sol: 49.88 %
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: 1.78→100 Å / Num. obs: 18975 / % possible obs: 97.9 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.04 / Χ2: 1.155 / Net I/av σ(I): 51.869 / Net I/σ(I): 15.9 / Num. measured all: 145509
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.78-1.817.80.3929290.983197.4
1.81-1.847.80.3410.968197.9
1.84-1.887.80.2790.972197.5
1.88-1.927.80.2380.998198.3
1.92-1.967.80.1990.988197.9
1.96-27.80.1610.983198.1
2-2.057.80.1230.964197.9
2.05-2.117.80.10.974198.4
2.11-2.177.80.0840.963198.5
2.17-2.247.80.0750.991198.3
2.24-2.327.70.0630.999199
2.32-2.427.80.0511.011198.6
2.42-2.537.70.0521.161198.9
2.53-2.667.70.0511.418199
2.66-2.837.70.0471.655199.2
2.83-3.047.70.0451.778199.3
3.04-3.357.70.0341.527199.3
3.35-3.837.60.0281.317199.4
3.83-4.837.30.0241.158197.6
4.83-1006.70.0241.312188.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.03 Å32.08 Å
Translation2.03 Å32.08 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: 1.78→32.08 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.468 / SU ML: 0.081 / SU R Cruickshank DPI: 0.1304 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.136
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2526 969 5.1 %RANDOM
Rwork0.1962 ---
obs0.199 18006 97.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 152.36 Å2 / Biso mean: 41.74 Å2 / Biso min: 13.89 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.78→32.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1462 0 33 36 1531
Biso mean--33.98 41.76 -
Num. residues----184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191551
X-RAY DIFFRACTIONr_bond_other_d0.0010.021487
X-RAY DIFFRACTIONr_angle_refined_deg2.0091.9752103
X-RAY DIFFRACTIONr_angle_other_deg0.98233409
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8465189
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.01522.83874
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.35315270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1281516
X-RAY DIFFRACTIONr_chiral_restr0.1210.2237
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021737
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02371
LS refinement shellResolution: 1.783→1.83 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 73 -
Rwork0.212 1314 -
all-1387 -
obs--95.92 %

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