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- PDB-9g51: Crystal structure of LmrR with V15 replaced by unnatural amino ac... -

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Basic information

Entry
Database: PDB / ID: 9g51
TitleCrystal structure of LmrR with V15 replaced by unnatural amino acid 4-mercaptophenylalanine, apo
ComponentsTranscriptional regulator, PadR-like family
KeywordsMETAL BINDING PROTEIN / Artificial metalloenzyme / unnatural amino acid / 4-mercaptophenylalanine / PadR-fold
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: 2.35 Å
AuthorsThunnissen, A.M.W.H. / Aalbers, F.S. / Veen, M.J. / Rozeboom, H.J. / Roelfes, G.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)885396European Union
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: Artificial Gold Enzymes Using a Genetically Encoded Thiophenol-Based Noble-Metal-Binding Ligand.
Authors: Veen, M.J. / Aalbers, F.S. / Rozeboom, H.J. / Thunnissen, A.W.H. / Sauer, D.F. / Roelfes, G.
History
DepositionJul 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.year / _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
B: Transcriptional regulator, PadR-like family


Theoretical massNumber of molelcules
Total (without water)29,6902
Polymers29,6902
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-22 kcal/mol
Surface area13430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.908, 34.988, 68.116
Angle α, β, γ (deg.)90.00, 97.18, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Transcriptional regulator, PadR-like family


Mass: 14844.896 Da / Num. of mol.: 2 / Mutation: V14 replaced with 4-mercaptophenylalanine
Source method: isolated from a genetically manipulated source
Details: LmrR carrying a C-terminal strep-tag and with V15 replaced with 4-mercaptophenylalanine
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.: 1 / 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: 2.06 Å3/Da / Density % sol: 40.27 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: Sitting drops prepared with protein solution (14 mg/ml protein in 150 mM NaCl, 25 mM Tris-HCl, pH 7.5, 0.5 mM TCEP) mixed with reservoir crystallization solution (16-21% PEG 3350, 0.2 M KSCN ...Details: Sitting drops prepared with protein solution (14 mg/ml protein in 150 mM NaCl, 25 mM Tris-HCl, pH 7.5, 0.5 mM TCEP) mixed with reservoir crystallization solution (16-21% PEG 3350, 0.2 M KSCN in 0.2 M Bis-Tris propane, pH 6.5-7.2)
PH range: 6.5 - 7.2

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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: May 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 2.35→67.59 Å / Num. obs: 10311 / % possible obs: 100 % / Redundancy: 4.4 % / CC1/2: 1 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.024 / Rrim(I) all: 0.05 / Χ2: 0.91 / Net I/σ(I): 13.3 / Num. measured all: 45074
Reflection shellResolution: 2.35→2.44 Å / % possible obs: 100 % / Redundancy: 4.4 % / Rmerge(I) obs: 1.273 / Num. measured all: 4622 / Num. unique obs: 1048 / CC1/2: 0.586 / Rpim(I) all: 0.677 / Rrim(I) all: 1.447 / Χ2: 0.91 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0419refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→67.58 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 24.47 / SU ML: 0.248 / Cross valid method: THROUGHOUT / ESU R: 0.424 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26238 504 4.9 %RANDOM
Rwork0.21712 ---
obs0.21936 9803 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 97.305 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å2-0 Å20.21 Å2
2---0.16 Å20 Å2
3----1.2 Å2
Refinement stepCycle: 1 / Resolution: 2.35→67.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1769 0 0 1 1770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0121809
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161765
X-RAY DIFFRACTIONr_angle_refined_deg1.9891.8592424
X-RAY DIFFRACTIONr_angle_other_deg0.7041.7984060
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4955214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.752514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.26410360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.3710.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022125
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02431
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_it8.647.334862
X-RAY DIFFRACTIONr_mcbond_other8.6357.334862
X-RAY DIFFRACTIONr_mcangle_it12.24413.1411074
X-RAY DIFFRACTIONr_mcangle_other12.23913.1441075
X-RAY DIFFRACTIONr_scbond_it10.5198.463947
X-RAY DIFFRACTIONr_scbond_other10.5138.464948
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other15.49515.0531351
X-RAY DIFFRACTIONr_long_range_B_refined18.28373.962076
X-RAY DIFFRACTIONr_long_range_B_other18.27973.972077
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 35 -
Rwork0.322 697 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.915-0.0905-1.17030.671-0.04191.6607-0.04030.02940.02710.1104-0.0476-0.19280.0907-0.12370.08790.0775-0.0457-0.05620.1065-0.03570.269115.7969-0.075510.6828
20.3177-0.04140.9450.18850.42954.9854-0.0959-0.1739-0.07830.05280.16060.0175-0.1002-0.42-0.06470.08710.03930.02740.3804-0.03940.0718.88072.895729.365
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 113
2X-RAY DIFFRACTION2B3 - 117

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