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- PDB-9dnh: RamR variant D2.3 complexed with 1-phenyl-dihydroisoquinoline -

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Basic information

Entry
Database: PDB / ID: 9dnh
TitleRamR variant D2.3 complexed with 1-phenyl-dihydroisoquinoline
ComponentsEngineered RamR variant D2.3
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: 2.37 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

Downloads & links

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Assembly

Deposited unit
A: Engineered RamR variant D2.3
B: Engineered RamR variant D2.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8993
Polymers43,6922
Non-polymers2071
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-23 kcal/mol
Surface area18490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.107, 57.107, 449.903
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Engineered RamR variant D2.3


Mass: 21845.822 Da / Num. of mol.: 2
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-A1BGD / 1-phenyl-3,4-dihydroisoquinoline


Mass: 207.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13N / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
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: 2.42 Å3/Da / Density % sol: 49.25 %
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: 2.37→449.9 Å / Num. obs: 19261 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 0.976 / Rmerge(I) obs: 0.336 / Rpim(I) all: 0.077 / Rrim(I) all: 0.345 / Net I/σ(I): 7.8 / Num. measured all: 384934
Reflection shellResolution: 2.37→2.41 Å / % possible obs: 99.7 % / Redundancy: 21 % / Rmerge(I) obs: 3.174 / Num. measured all: 18877 / Num. unique obs: 899 / CC1/2: 0.424 / Rpim(I) all: 0.705 / Rrim(I) all: 3.253 / Net I/σ(I) obs: 0.9

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Processing

Software
NameVersionClassification
PHENIX1.18rc3_3805refinement
xia2data scaling
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→49.46 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3261 1910 10 %
Rwork0.2671 --
obs0.2728 19096 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.37→49.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2876 0 16 42 2934
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062948
X-RAY DIFFRACTIONf_angle_d1.0083991
X-RAY DIFFRACTIONf_dihedral_angle_d13.86402
X-RAY DIFFRACTIONf_chiral_restr0.052448
X-RAY DIFFRACTIONf_plane_restr0.009517
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.430.39131270.37051145X-RAY DIFFRACTION99
2.43-2.490.4231340.35771200X-RAY DIFFRACTION100
2.49-2.570.34371300.31661172X-RAY DIFFRACTION100
2.57-2.650.35191330.32391198X-RAY DIFFRACTION100
2.65-2.740.41311340.3231202X-RAY DIFFRACTION100
2.74-2.850.37411340.32131209X-RAY DIFFRACTION100
2.85-2.980.36271310.31531175X-RAY DIFFRACTION100
2.98-3.140.33991340.29021212X-RAY DIFFRACTION100
3.14-3.340.36061370.28141219X-RAY DIFFRACTION100
3.34-3.60.32851360.26551236X-RAY DIFFRACTION100
3.6-3.960.30871370.24911229X-RAY DIFFRACTION100
3.96-4.530.30321390.24141257X-RAY DIFFRACTION100
4.53-5.710.31011460.25361307X-RAY DIFFRACTION100
5.71-49.460.28571580.22721425X-RAY DIFFRACTION100

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