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- PDB-6ko8: Crystal structure of the Cholic acid bound RamR determined with X... -

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Basic information

Entry
Database: PDB / ID: 6ko8
TitleCrystal structure of the Cholic acid bound RamR determined with XtaLAB Synergy
ComponentsPutative regulatory protein
KeywordsDNA BINDING PROTEIN / multisite binding pocket / HTH-MOTIF
Function / homology
Function and homology information


DNA binding / RNA binding
Similarity search - Function
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 / Transcriptional regulator RamR
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. 14028S (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
Model detailsframework as crystalline sponge method
AuthorsMatsumoto, T. / Nakashima, R. / Yamano, A. / Nishino, K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: Development of a structure determination method using a multidrug-resistance regulator protein as a framework.
Authors: Matsumoto, T. / Nakashima, R. / Yamano, A. / Nishino, K.
History
DepositionAug 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 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

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Assembly

Deposited unit
A: Putative regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5493
Polymers22,0441
Non-polymers5052
Water1,69394
1
A: Putative regulatory protein
hetero molecules

A: Putative 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 area4280 Å2
ΔGint-43 kcal/mol
Surface area18710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.690, 53.897, 44.223
Angle α, β, γ (deg.)90.000, 93.060, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Putative regulatory protein


Mass: 22044.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S (bacteria)
Strain: 14028s / SGSC 2262 / Gene: STM14_0676 / Plasmid: PET DUET / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A0A0F6AY66, UniProt: Q8ZR43*PLUS
#2: Chemical ChemComp-CHD / CHOLIC ACID


Mass: 408.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H40O5 / 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.: 94 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 49.89 % / Mosaicity: 0.81 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: PEG3350, ammonium sulfate, sodium Citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5406 Å
DetectorType: RIGAKU HyPic-6000HE / Detector: PIXEL / Date: Nov 25, 2016
RadiationMonochromator: multi-layer mirror optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 1.55→22.09 Å / Num. obs: 29492 / % possible obs: 99.6 % / Redundancy: 4.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.015 / Rrim(I) all: 0.037 / Net I/σ(I): 16.6
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 3 % / Rmerge(I) obs: 0.637 / Num. unique obs: 1438 / CC1/2: 0.645 / Rpim(I) all: 0.424 / Rrim(I) all: 0.772 / % possible all: 97.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.29data scaling
MOLREPphasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
CrysalisProdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VVY

3vvy


Resolution: 1.55→22.09 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.963 / SU B: 4.281 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.076
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2038 1533 5.2 %RANDOM
Rwork0.1461 ---
obs0.1491 27959 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 126.64 Å2 / Biso mean: 35.451 Å2 / Biso min: 13.39 Å2
Baniso -1Baniso -2Baniso -3
1--2.54 Å20 Å20.83 Å2
2--2.16 Å20 Å2
3---0.29 Å2
Refinement stepCycle: final / Resolution: 1.55→22.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1447 0 34 94 1575
Biso mean--41.97 47.7 -
Num. residues----185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131508
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171408
X-RAY DIFFRACTIONr_angle_refined_deg1.8551.6382044
X-RAY DIFFRACTIONr_angle_other_deg1.6311.5733243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8045184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.72621.2282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1915256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0671513
X-RAY DIFFRACTIONr_chiral_restr0.0910.2210
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021668
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02335
X-RAY DIFFRACTIONr_rigid_bond_restr4.72932915
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 108 -
Rwork0.255 2015 -
all-2123 -
obs--97.7 %

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