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- PDB-9dnc: Apo crystal structure of RamR variant D2.1 -

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Basic information

Entry
Database: PDB / ID: 9dnc
TitleApo crystal structure of RamR variant D2.1
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: 1.9 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
B: Transcriptional regulator RamR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3804
Polymers44,3092
Non-polymers712
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-42 kcal/mol
Surface area18680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.820, 150.400, 39.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 22154.441 Da / Num. of mol.: 2
Mutation: Val inserted between residues 1 and 2, C134I, S137K, V138R (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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.06 Å3/Da / Density % sol: 59.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1M Sodium Acetate pH 4.6, 2.0M NaCl

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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: Jan 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.9→43.89 Å / Num. obs: 43806 / % possible obs: 99.8 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.03 / Rrim(I) all: 0.075 / Χ2: 0.99 / Net I/σ(I): 13.2 / Num. measured all: 280002
Reflection shellResolution: 1.9→1.95 Å / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 1.226 / Num. measured all: 21038 / Num. unique obs: 3183 / CC1/2: 0.532 / Rpim(I) all: 0.516 / Rrim(I) all: 1.332 / Χ2: 0.78 / 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: 1.9→43.89 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2157 3776 4.57 %
Rwork0.1968 --
obs0.1977 43742 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→43.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2938 0 2 188 3128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153048
X-RAY DIFFRACTIONf_angle_d1.2234112
X-RAY DIFFRACTIONf_dihedral_angle_d22.8911149
X-RAY DIFFRACTIONf_chiral_restr0.069453
X-RAY DIFFRACTIONf_plane_restr0.015529
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.34751340.33752872X-RAY DIFFRACTION100
1.92-1.950.34091400.30882963X-RAY DIFFRACTION100
1.95-1.980.36991470.28622966X-RAY DIFFRACTION100
1.98-20.27551380.26812864X-RAY DIFFRACTION100
2-2.030.24081360.24682884X-RAY DIFFRACTION100
2.03-2.070.28831410.23622976X-RAY DIFFRACTION100
2.07-2.10.27371450.23752948X-RAY DIFFRACTION100
2.1-2.140.25981350.22242885X-RAY DIFFRACTION100
2.14-2.170.20781450.22112932X-RAY DIFFRACTION100
2.17-2.220.24441400.20822964X-RAY DIFFRACTION100
2.22-2.260.21141360.20322898X-RAY DIFFRACTION100
2.26-2.310.27061410.20672954X-RAY DIFFRACTION100
2.31-2.360.2181400.19492916X-RAY DIFFRACTION100
2.37-2.420.21181360.2022887X-RAY DIFFRACTION100
2.42-2.490.24521470.19512984X-RAY DIFFRACTION100
2.49-2.560.26771320.21112864X-RAY DIFFRACTION100
2.56-2.650.23431430.21142981X-RAY DIFFRACTION100
2.65-2.740.21561360.21022893X-RAY DIFFRACTION100
2.74-2.850.26751460.20722958X-RAY DIFFRACTION100
2.85-2.980.28361390.22622871X-RAY DIFFRACTION100
2.98-3.140.21861300.20352934X-RAY DIFFRACTION100
3.14-3.330.21021380.20382954X-RAY DIFFRACTION99
3.33-3.590.23741420.18522903X-RAY DIFFRACTION99
3.59-3.950.16591420.17132919X-RAY DIFFRACTION99
3.95-4.520.16871430.1642874X-RAY DIFFRACTION99
4.52-5.690.19441380.18522895X-RAY DIFFRACTION99
5.7-43.890.19181460.18312865X-RAY DIFFRACTION98

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