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- PDB-9dnk: RamR variant R2.1 complexed with 1R-1-phenyl-1,2,3,4-tetrahydrois... -

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Basic information

Entry
Database: PDB / ID: 9dnk
TitleRamR variant R2.1 complexed with 1R-1-phenyl-1,2,3,4-tetrahydroisoquinoline
ComponentsEngineered RamR Variant R2.1
KeywordsTRANSCRIPTION / Directed evolution / Transcription factor / Stereoselectivity
Function / homology:
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKim, W. / Zhang, Y.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM148356 United States
CitationJournal: To be published
Title: Using stereoselective biosensors to evolve asymmetric biocatalysts
Authors: d'Oelsnitz, S. / Kim, W. / Taghon, G. / Hardtke, H. / Ikonomova, S.P. / Alperovich, N. / Vasilyeva, O. / James, M.J. / Zigon, E.S. / Johnson, C. / Ellington, A.D. / Zhang, Y.J. / Springer, M. ...Authors: d'Oelsnitz, S. / Kim, W. / Taghon, G. / Hardtke, H. / Ikonomova, S.P. / Alperovich, N. / Vasilyeva, O. / James, M.J. / Zigon, E.S. / Johnson, C. / Ellington, A.D. / Zhang, Y.J. / Springer, M. / Silver, P.A. / Ross, D.
History
DepositionSep 17, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Engineered RamR Variant R2.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0892
Polymers21,8801
Non-polymers2091
Water00
1
A: Engineered RamR Variant R2.1
hetero molecules

A: Engineered RamR Variant R2.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1784
Polymers43,7602
Non-polymers4192
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3610 Å2
ΔGint-21 kcal/mol
Surface area18500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.690, 93.394, 44.610
Angle α, β, γ (deg.)90.00, 93.76, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Engineered RamR Variant R2.1


Mass: 21879.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-A1BEC / (1R)-1-phenyl-1,2,3,4-tetrahydroisoquinoline


Mass: 209.286 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H15N / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 2.79 Å3/Da / Density % sol: 55.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1M NaCl, 0.2M Ammonium Sulfate, 0.1M MES pH 6.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 8122 / % possible obs: 97.6 % / Redundancy: 2.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.096 / Net I/σ(I): 12.3
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 1.01 / Num. unique obs: 390 / CC1/2: 0.294

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Processing

Software
NameVersionClassification
PHENIX1.18rc3_3805refinement
DIALSdata scaling
DIALSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→49.62 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 39.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2674 414 5.2 %
Rwork0.2267 --
obs0.2289 7968 95.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→49.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1473 0 16 0 1489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091520
X-RAY DIFFRACTIONf_angle_d1.0792053
X-RAY DIFFRACTIONf_dihedral_angle_d14.056206
X-RAY DIFFRACTIONf_chiral_restr0.051223
X-RAY DIFFRACTIONf_plane_restr0.008268
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.860.38481310.31942402X-RAY DIFFRACTION92
2.86-3.60.3061290.25732591X-RAY DIFFRACTION98
3.61-49.620.23911540.19822561X-RAY DIFFRACTION96

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