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- PDB-9gtv: Crystal structure of RamR with Tyr59 replaced with para-boronophe... -

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Basic information

Entry
Database: PDB / ID: 9gtv
TitleCrystal structure of RamR with Tyr59 replaced with para-boronophenylalanine (boronate form)
ComponentsTranscriptional regulator RamR
KeywordsDNA BINDING PROTEIN / Artificial enzyme / TetR family / boron designer enzyme / noncanonical amino acid / para-boronophenylalanine / boron acid catalysis
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: 2.78 Å
AuthorsLongwitz, L. / Brouwer, B. / Thunnissen, A.M.W.H. / Roelfes, G.
Funding supportEuropean Union, Netherlands, 2items
OrganizationGrant numberCountry
European Research Council (ERC)885396European Union
Netherlands Organisation for Scientific Research (NWO)OCENW.KLEIN.143 Netherlands
CitationJournal: Acs Catalysis / Year: 2024
Title: Boron Designer Enzyme with a Hybrid Catalytic Dyad.
Authors: Longwitz, L. / Kamer, M.D. / Brouwer, B. / Thunnissen, A.W.H. / Roelfes, G.
History
DepositionSep 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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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
C: Transcriptional regulator RamR
D: Transcriptional regulator RamR


Theoretical massNumber of molelcules
Total (without water)92,4404
Polymers92,4404
Non-polymers00
Water00
1
A: Transcriptional regulator RamR
B: Transcriptional regulator RamR


Theoretical massNumber of molelcules
Total (without water)46,2202
Polymers46,2202
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Transcriptional regulator RamR

C: Transcriptional regulator RamR


Theoretical massNumber of molelcules
Total (without water)46,2202
Polymers46,2202
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,y-1/2,-z1
Unit cell
Length a, b, c (Å)78.872, 51.880, 118.319
Angle α, β, γ (deg.)90.00, 96.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 23110.066 Da / Num. of mol.: 4 / Mutation: Y59pBoF, C67S, C134S
Source method: isolated from a genetically manipulated source
Details: RamR carrying a C-terminal Strep II tag. Residue 59 replaced by pBoF (para-boronophenylalanine)
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: ramR, STM0580 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZR43
Has ligand of interestY
Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 52.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein solution: 13 mg/ml in 20 mM Hepes, pH 8, 500 mM NaCl. Reservoir solution: 0.1 M Tris, pH 8.5, 20% ethanol. Drops of 200 nL were prepared by mixing protein solution and reservoir solution (1:1)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 2.78→78 Å / Num. obs: 22672 / % possible obs: 93.4 % / Redundancy: 2.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.051 / Rrim(I) all: 0.091 / Χ2: 0.9 / Net I/σ(I): 8.5
Reflection shellResolution: 2.78→2.93 Å / % possible obs: 64.3 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.457 / Num. measured all: 4250 / Num. unique obs: 2241 / CC1/2: 0.684 / Rpim(I) all: 0.399 / Rrim(I) all: 0.61 / Χ2: 0.69 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.21.1_5286refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.78→78 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 31.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2568 1186 5.23 %RANDOM
Rwork0.2105 ---
obs0.2129 22661 93.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.78→78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5934 0 0 0 5934
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016038
X-RAY DIFFRACTIONf_angle_d1.2158147
X-RAY DIFFRACTIONf_dihedral_angle_d15.5622231
X-RAY DIFFRACTIONf_chiral_restr0.052905
X-RAY DIFFRACTIONf_plane_restr0.0121048
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.78-2.910.4007940.31291692X-RAY DIFFRACTION59
2.91-3.060.34541640.28512670X-RAY DIFFRACTION94
3.06-3.260.31411520.27882858X-RAY DIFFRACTION100
3.26-3.510.31881510.24062821X-RAY DIFFRACTION99
3.51-3.860.29611600.21572824X-RAY DIFFRACTION99
3.86-4.420.25341550.20042836X-RAY DIFFRACTION99
4.42-5.570.22171460.19292858X-RAY DIFFRACTION98
5.57-780.21041640.18272916X-RAY DIFFRACTION98

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