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- PDB-9dn8: RamR variant S2.3 complexed with 1S-1-phenyl-1,2,3,4-tetrahydrois... -

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Basic information

Entry
Database: PDB / ID: 9dn8
TitleRamR variant S2.3 complexed with 1S-1-phenyl-1,2,3,4-tetrahydroisoquinoline
ComponentsTranscriptional regulator RamR
KeywordsTRANSCRIPTION / Directed evolution / Transcription factor / Stereoselectivity
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. / : / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily
Similarity search - Domain/homology
: / Transcriptional regulator RamR
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 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: Transcriptional regulator RamR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4665
Polymers21,8551
Non-polymers6114
Water88349
1
A: Transcriptional regulator RamR
hetero molecules

A: Transcriptional regulator RamR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,93110
Polymers43,7102
Non-polymers1,2218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area5070 Å2
ΔGint-91 kcal/mol
Surface area17880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.460, 64.460, 100.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-442-

HOH

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Components

#1: Protein Transcriptional regulator RamR / HTH-type transcriptional regulator RamR / Local repressor of ramA


Mass: 21855.025 Da / Num. of mol.: 1
Mutation: Val inserted between residues 1 and 2, C134E, S137E (Uniprot numbering)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: ramR, STM0580 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZR43
#2: Chemical ChemComp-A1BED / (1S)-1-phenyl-1,2,3,4-tetrahydroisoquinoline


Mass: 209.286 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H15N / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.38 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1M NaCl, 0.2M Ammounium Sulfate, 0.1M MES pH 6.5, 20% 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: 2.12→50.15 Å / Num. obs: 12617 / % possible obs: 100 % / Redundancy: 13.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.038 / Rrim(I) all: 0.143 / Χ2: 0.98 / Net I/σ(I): 14.4 / Num. measured all: 173658
Reflection shellResolution: 2.12→2.18 Å / % possible obs: 100 % / Redundancy: 13.5 % / Rmerge(I) obs: 1.496 / Num. measured all: 12173 / Num. unique obs: 902 / CC1/2: 0.668 / Rpim(I) all: 0.418 / Rrim(I) all: 1.555 / Χ2: 0.93 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
PHENIX1.18rc3_3805refinement
Aimlessdata scaling
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→45.58 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2362 2281 9.96 %
Rwork0.1983 --
obs0.2021 12566 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.12→45.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1483 0 42 49 1574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021553
X-RAY DIFFRACTIONf_angle_d0.472094
X-RAY DIFFRACTIONf_dihedral_angle_d13.319211
X-RAY DIFFRACTIONf_chiral_restr0.032227
X-RAY DIFFRACTIONf_plane_restr0.002267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.170.34941430.2981289X-RAY DIFFRACTION100
2.17-2.220.3251430.27781293X-RAY DIFFRACTION100
2.22-2.270.31051430.26591259X-RAY DIFFRACTION100
2.27-2.330.28871460.26031297X-RAY DIFFRACTION100
2.33-2.40.33131360.23391303X-RAY DIFFRACTION100
2.4-2.480.25381400.22791306X-RAY DIFFRACTION100
2.48-2.570.23831390.22351262X-RAY DIFFRACTION100
2.57-2.670.27971460.23211298X-RAY DIFFRACTION100
2.67-2.790.27091390.21511291X-RAY DIFFRACTION100
2.79-2.940.26151480.21071300X-RAY DIFFRACTION100
2.94-3.120.20371390.20461270X-RAY DIFFRACTION100
3.12-3.360.25241420.20521287X-RAY DIFFRACTION100
3.37-3.70.2451400.17461293X-RAY DIFFRACTION100
3.7-4.240.22571440.16611295X-RAY DIFFRACTION100
4.24-5.340.20321440.16811287X-RAY DIFFRACTION100
5.34-45.580.18521490.18441284X-RAY DIFFRACTION100

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