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- PDB-9dnl: Apo crystal structure of RamR variant R2.2 -

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Basic information

Entry
Database: PDB / ID: 9dnl
TitleApo crystal structure of RamR variant R2.2
ComponentsEngineered RamR variant R2.2
KeywordsTRANSCRIPTION / Directed evolution / Transcription factor / Stereoselectivity
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.01 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 R2.2
B: Engineered RamR variant R2.2
C: Engineered RamR variant R2.2
D: Engineered RamR variant R2.2


Theoretical massNumber of molelcules
Total (without water)88,4734
Polymers88,4734
Non-polymers00
Water00
1
A: Engineered RamR variant R2.2
B: Engineered RamR variant R2.2


Theoretical massNumber of molelcules
Total (without water)44,2362
Polymers44,2362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-16 kcal/mol
Surface area18660 Å2
MethodPISA
2
C: Engineered RamR variant R2.2
D: Engineered RamR variant R2.2


Theoretical massNumber of molelcules
Total (without water)44,2362
Polymers44,2362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-18 kcal/mol
Surface area18780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.680, 95.220, 130.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Engineered RamR variant R2.2


Mass: 22118.139 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Production host: Escherichia coli (E. coli)
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: 3.32 Å3/Da / Density % sol: 62.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1M TRIS pH 8.5, 15% PEG 20000

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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: Dec 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 3.89→93.92 Å / Num. obs: 11071 / % possible obs: 99.9 % / Redundancy: 6.3 % / CC1/2: 0.975 / Rmerge(I) obs: 0.547 / Rpim(I) all: 0.236 / Rrim(I) all: 0.597 / Χ2: 0.99 / Net I/σ(I): 3.2 / Num. measured all: 69577
Reflection shellResolution: 3.89→3.99 Å / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 3.654 / Num. measured all: 5160 / Num. unique obs: 804 / CC1/2: 0.264 / Rpim(I) all: 1.554 / Rrim(I) all: 3.977 / Χ2: 1.01 / Net I/σ(I) obs: 0.7

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Processing

Software
NameVersionClassification
PHENIX1.18rc3_3805refinement
Aimlessdata scaling
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.01→65.08 Å / SU ML: 0.79 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2947 1647 10 %
Rwork0.2525 --
obs0.257 9361 86.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.01→65.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5728 0 0 0 5728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045834
X-RAY DIFFRACTIONf_angle_d0.6977866
X-RAY DIFFRACTIONf_dihedral_angle_d32.2162114
X-RAY DIFFRACTIONf_chiral_restr0.042882
X-RAY DIFFRACTIONf_plane_restr0.0161008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.01-4.130.40781190.34631111X-RAY DIFFRACTION77
4.13-4.260.37421120.33551111X-RAY DIFFRACTION77
4.26-4.410.30851140.32661149X-RAY DIFFRACTION81
4.41-4.590.37391300.30621193X-RAY DIFFRACTION82
4.59-4.80.31371320.2871184X-RAY DIFFRACTION82
4.8-5.050.32151460.2811299X-RAY DIFFRACTION92
5.05-5.370.3251520.28531310X-RAY DIFFRACTION92
5.37-5.780.31511410.29521310X-RAY DIFFRACTION92
5.78-6.360.33151580.27751283X-RAY DIFFRACTION91
6.37-7.280.30741590.26831311X-RAY DIFFRACTION91
7.28-9.160.22721360.19471286X-RAY DIFFRACTION91
9.18-65.080.2341480.16941272X-RAY DIFFRACTION89

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