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- PDB-9dn9: RamR variant S2.4 complexed with 1S-1-phenyl-1,2,3,4-tetrahydrois... -

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Basic information

Entry
Database: PDB / ID: 9dn9
TitleRamR variant S2.4 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: 1.8 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
B: Transcriptional regulator RamR
C: Transcriptional regulator RamR
D: Transcriptional regulator RamR
A: Transcriptional regulator RamR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,58912
Polymers87,3684
Non-polymers1,2218
Water6,774376
1
B: Transcriptional regulator RamR
C: Transcriptional regulator RamR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2956
Polymers43,6842
Non-polymers6114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-62 kcal/mol
Surface area17840 Å2
MethodPISA
2
D: Transcriptional regulator RamR
A: Transcriptional regulator RamR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2956
Polymers43,6842
Non-polymers6114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-62 kcal/mol
Surface area17730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.170, 54.360, 91.540
Angle α, β, γ (deg.)75.74, 81.98, 89.93
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 21841.988 Da / Num. of mol.: 4
Mutation: Val inserted between residues 1 and 2, C134E, S137Q, V138S (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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-A1BED / (1S)-1-phenyl-1,2,3,4-tetrahydroisoquinoline


Mass: 209.286 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H15N / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.41 Å3/Da / Density % sol: 49.02 %
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: 1.8→40.89 Å / Num. obs: 71463 / % possible obs: 94.4 % / Redundancy: 2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.067 / Rrim(I) all: 0.1 / Χ2: 0.92 / Net I/σ(I): 7 / Num. measured all: 141355
Reflection shellResolution: 1.8→1.85 Å / % possible obs: 94.7 % / Redundancy: 2 % / Rmerge(I) obs: 0.65 / Num. measured all: 10624 / Num. unique obs: 5353 / CC1/2: 0.452 / Rpim(I) all: 0.589 / Rrim(I) all: 0.879 / Χ2: 0.88 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX1.18rc3_3805refinement
Aimlessdata scaling
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→40.89 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2636 3542 2.85 %
Rwork0.2352 --
obs0.236 71458 81.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→40.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5877 0 84 376 6337
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056069
X-RAY DIFFRACTIONf_angle_d0.7858180
X-RAY DIFFRACTIONf_dihedral_angle_d23.182228
X-RAY DIFFRACTIONf_chiral_restr0.044893
X-RAY DIFFRACTIONf_plane_restr0.0051050
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.4191410.36924735X-RAY DIFFRACTION80
1.82-1.850.38951390.36044807X-RAY DIFFRACTION81
1.85-1.880.34541380.35554741X-RAY DIFFRACTION81
1.88-1.910.35871430.33654776X-RAY DIFFRACTION81
1.91-1.940.34921620.31524792X-RAY DIFFRACTION82
1.94-1.970.35881190.29644739X-RAY DIFFRACTION81
1.97-2.010.31791480.29744900X-RAY DIFFRACTION82
2.01-2.050.27271440.27594729X-RAY DIFFRACTION82
2.05-2.090.29781450.27064898X-RAY DIFFRACTION82
2.09-2.130.35951340.26344791X-RAY DIFFRACTION82
2.13-2.180.27181530.2654908X-RAY DIFFRACTION82
2.18-2.240.33041270.25564701X-RAY DIFFRACTION81
2.24-2.30.28241360.254775X-RAY DIFFRACTION81
2.3-2.370.26521450.24334727X-RAY DIFFRACTION80
2.37-2.440.23471520.23564875X-RAY DIFFRACTION83
2.44-2.530.28651430.24084813X-RAY DIFFRACTION82
2.53-2.630.24981260.24594822X-RAY DIFFRACTION82
2.63-2.750.26271510.24594877X-RAY DIFFRACTION82
2.75-2.90.22341370.23584947X-RAY DIFFRACTION84
2.9-3.080.23081390.22794821X-RAY DIFFRACTION82
3.08-3.320.24291420.21834922X-RAY DIFFRACTION84
3.32-3.650.23911560.20354890X-RAY DIFFRACTION82
3.65-4.180.26391380.19154824X-RAY DIFFRACTION83
4.18-5.260.22561490.1994855X-RAY DIFFRACTION83
5.26-40.890.25261350.21534961X-RAY DIFFRACTION84

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