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- PDB-6ko7: Crystal structure of the Ethidium bound RamR determined with XtaL... -

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Basic information

Entry
Database: PDB / ID: 6ko7
TitleCrystal structure of the Ethidium 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
ETHIDIUM / 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: 1.7 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
B: Putative regulatory protein
C: Putative regulatory protein
D: Putative regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,81912
Polymers88,1774
Non-polymers1,6428
Water5,657314
1
A: Putative regulatory protein
B: Putative regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9096
Polymers44,0892
Non-polymers8214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-54 kcal/mol
Surface area17430 Å2
MethodPISA
2
C: Putative regulatory protein
D: Putative regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9096
Polymers44,0892
Non-polymers8214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-53 kcal/mol
Surface area17630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.164, 54.276, 91.412
Angle α, β, γ (deg.)103.420, 97.450, 90.140
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Putative regulatory protein


Mass: 22044.262 Da / Num. of mol.: 4
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-ET / ETHIDIUM


Mass: 314.404 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H20N3 / Feature type: SUBJECT OF INVESTIGATION
#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.: 314 / 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: 2.53 Å3/Da / Density % sol: 51.3 % / Mosaicity: 0.85 °
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: Sep 15, 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: 1.7→23.45 Å / Num. obs: 88793 / % possible obs: 98.7 % / Redundancy: 2.4 % / CC1/2: 0.994 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.047 / Rrim(I) all: 0.084 / Net I/σ(I): 7.2
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.402 / Num. unique obs: 4303 / CC1/2: 0.479 / Rpim(I) all: 0.371 / Rrim(I) all: 0.548 / % possible all: 94.8

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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: 1.7→23.45 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.82 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.111
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2348 4325 4.9 %RANDOM
Rwork0.1685 ---
obs0.1718 84464 98.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 77.73 Å2 / Biso mean: 25.753 Å2 / Biso min: 12.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0.09 Å20.28 Å2
2---0.15 Å2-0.26 Å2
3---0.35 Å2
Refinement stepCycle: final / Resolution: 1.7→23.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5854 0 116 314 6284
Biso mean--23.96 35.06 -
Num. residues----737
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0136082
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175672
X-RAY DIFFRACTIONr_angle_refined_deg1.8451.6398212
X-RAY DIFFRACTIONr_angle_other_deg1.5591.57613022
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8485733
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.51520.69348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.067151061
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6761560
X-RAY DIFFRACTIONr_chiral_restr0.0920.2793
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026847
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021437
X-RAY DIFFRACTIONr_rigid_bond_restr3.409311754
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 331 -
Rwork0.263 6015 -
all-6346 -
obs--95.44 %

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