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- PDB-9h87: Crystal structure of LmrR variant V15aY with Val15 replaced by 3-... -

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Basic information

Entry
Database: PDB / ID: 9h87
TitleCrystal structure of LmrR variant V15aY with Val15 replaced by 3-aminotyrosine
ComponentsTranscriptional regulator, PadR-like family
KeywordsDNA BINDING PROTEIN / Artificial enzyme / Friedel-Crafts alkylase / unnatural amino acid / 3-aminotyrosine
Function / homology: / Transcription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Transcriptional regulator, PadR-like family
Function and homology information
Biological speciesLactococcus cremoris subsp. cremoris MG1363 (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsThunnissen, A.M.W.H. / Brouwer, B. / 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: Chem Sci / Year: 2025
Title: Genetically encoded 3-aminotyrosine as catalytic residue in a designer Friedel-Crafts alkylase.
Authors: Brouwer, B. / Della-Felice, F. / Thunnissen, A.W.H. / Roelfes, G.
History
DepositionOct 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 4, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator, PadR-like family


Theoretical massNumber of molelcules
Total (without water)15,0701
Polymers15,0701
Non-polymers00
Water905
1
A: Transcriptional regulator, PadR-like family

A: Transcriptional regulator, PadR-like family


Theoretical massNumber of molelcules
Total (without water)30,1402
Polymers30,1402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554-x+y,y,-z-1/31
Buried area2840 Å2
ΔGint-22 kcal/mol
Surface area13680 Å2
Unit cell
Length a, b, c (Å)70.714, 70.714, 59.838
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

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Components

#1: Protein Transcriptional regulator, PadR-like family


Mass: 15069.849 Da / Num. of mol.: 1 / Mutation: V15(3-amino-Y),K55D,K59Q
Source method: isolated from a genetically manipulated source
Details: LmrR carrying a C-terminal strep-II tag and with V15 replaced by 3-aminotyrosine
Source: (gene. exp.) Lactococcus cremoris subsp. cremoris MG1363 (lactic acid bacteria)
Gene: llmg_0323 / Production host: Escherichia coli (E. coli) / References: UniProt: A2RI36
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
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: 2.87 Å3/Da / Density % sol: 57.08 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: The protein solution contained 16 mg/ml protein in 20 mM HEPES, 280 mM NaCl, pH 7.0. The reservoir solution contained 0.2 M KSCN, 0.1 M Bis-Tris propane, pH 6.5, 20% (w/v) PEG 3350
PH range: 6.5

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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: Nov 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 2.15→61.26 Å / Num. obs: 9471 / % possible obs: 100 % / Redundancy: 10.2 % / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.016 / Rrim(I) all: 0.053 / Χ2: 0.95 / Net I/σ(I): 17.4 / Num. measured all: 96934
Reflection shellResolution: 2.15→2.21 Å / % possible obs: 100 % / Redundancy: 10.3 % / Rmerge(I) obs: 1.854 / Num. measured all: 7881 / Num. unique obs: 765 / CC1/2: 0.705 / Rpim(I) all: 0.603 / Rrim(I) all: 1.951 / Χ2: 0.91 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→42.84 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 16.705 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26819 474 5 %RANDOM
Rwork0.22122 ---
obs0.22357 8993 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.912 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å2-0.6 Å2-0 Å2
2---1.21 Å20 Å2
3---3.92 Å2
Refinement stepCycle: 1 / Resolution: 2.15→42.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms928 0 0 5 933
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.012942
X-RAY DIFFRACTIONr_bond_other_d0.0010.016898
X-RAY DIFFRACTIONr_angle_refined_deg1.9851.8441266
X-RAY DIFFRACTIONr_angle_other_deg0.6971.7912062
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2945112
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.61957
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.53610181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1020.2134
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021124
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02224
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.7965.405451
X-RAY DIFFRACTIONr_mcbond_other5.765.41451
X-RAY DIFFRACTIONr_mcangle_it7.7819.644562
X-RAY DIFFRACTIONr_mcangle_other7.7919.656563
X-RAY DIFFRACTIONr_scbond_it6.5025.953491
X-RAY DIFFRACTIONr_scbond_other6.4975.96492
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.1410.617705
X-RAY DIFFRACTIONr_long_range_B_refined12.82164.533865
X-RAY DIFFRACTIONr_long_range_B_other12.81964.543866
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.205 Å
RfactorNum. reflection% reflection
Rfree0.315 30 -
Rwork0.322 673 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -10.5999 Å / Origin y: 17.9777 Å / Origin z: -8.8207 Å
111213212223313233
T0.0333 Å2-0.0415 Å2-0.0481 Å2-0.1776 Å2-0.0157 Å2--0.3549 Å2
L2.6799 °2-0.768 °2-1.5024 °2-0.6164 °20.2991 °2--0.898 °2
S-0.0883 Å °0.146 Å °-0.3309 Å °0.098 Å °-0.0447 Å °0.0712 Å °0.0349 Å °-0.0744 Å °0.133 Å °

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