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- PDB-9g52: Crystal structure of LmrR with V15 replaced by unnatural amino ac... -

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Basic information

Entry
Database: PDB / ID: 9g52
TitleCrystal structure of LmrR with V15 replaced by unnatural amino acid 4-mercaptophenylalanine, Au(I) bound
ComponentsTranscriptional regulator, PadR-like family
KeywordsMETAL BINDING PROTEIN / Artificial metalloenzyme / unnatural amino acid / 4-mercaptophenylalanine / gold-bound
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: 2.5 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8873
Polymers29,6902
Non-polymers1971
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-28 kcal/mol
Surface area13290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.440, 52.715, 146.194
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 Transcriptional regulator, PadR-like family


Mass: 14844.896 Da / Num. of mol.: 2 / Mutation: V15 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: Chemical ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Au / Feature type: SUBJECT OF INVESTIGATION
#3: 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: 2.3 Å3/Da / Density % sol: 46.52 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Sitting drops prepared with protein solution (0.412 mM protein, 0.824 mM KAuCN2, 20 mM MOPS, pH 7.0, 150 mM NaCl) and reservoir crystallization solution (0.2 M NaF, 0.1 M Bis-Tris propane, pH 7.5, 20% PEG 3350)

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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: 2.5→48.73 Å / Num. obs: 10107 / % possible obs: 100 % / Redundancy: 9.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.041 / Rrim(I) all: 0.127 / Χ2: 1 / Net I/σ(I): 11.1 / Num. measured all: 94882
Reflection shellResolution: 2.5→2.6 Å / % possible obs: 100 % / Redundancy: 8.6 % / Rmerge(I) obs: 1.34 / Num. measured all: 9546 / Num. unique obs: 1109 / CC1/2: 0.726 / Rpim(I) all: 0.482 / Rrim(I) all: 1.427 / Χ2: 0.94 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0419refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→42.79 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.918 / SU B: 43.935 / SU ML: 0.402 / Cross valid method: THROUGHOUT / ESU R: 0.564 / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29397 521 5.2 %RANDOM
Rwork0.24514 ---
obs0.24783 9540 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.172 Å2
Baniso -1Baniso -2Baniso -3
1--5.75 Å20 Å20 Å2
2--10.21 Å20 Å2
3----4.46 Å2
Refinement stepCycle: 1 / Resolution: 2.5→42.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1824 0 1 1 1826
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121851
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161800
X-RAY DIFFRACTIONr_angle_refined_deg1.8171.8542482
X-RAY DIFFRACTIONr_angle_other_deg0.6791.7964138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1245219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.07514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.80710365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.3510.2265
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022179
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02437
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_it6.5515.877885
X-RAY DIFFRACTIONr_mcbond_other6.5195.878885
X-RAY DIFFRACTIONr_mcangle_it9.75410.5291101
X-RAY DIFFRACTIONr_mcangle_other9.7510.5361102
X-RAY DIFFRACTIONr_scbond_it7.5066.725966
X-RAY DIFFRACTIONr_scbond_other7.5026.728967
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.08311.9951383
X-RAY DIFFRACTIONr_long_range_B_refined15.33660.612177
X-RAY DIFFRACTIONr_long_range_B_other15.33660.622178
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 50 -
Rwork0.368 674 -
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)
11.38360.1986-0.09830.0805-0.02273.068-0.01310.19950.06390.02940.04660.05390.04950.2307-0.03350.02160.02240.02770.07960.03340.044413.015210.203714.9304
20.6241-0.44-0.53190.65960.96442.105-0.1037-0.147-0.135-0.00270.030.1411-0.06490.29460.07360.09770.0049-0.01780.1474-0.00890.06638.434814.871633.8029
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 115
2X-RAY DIFFRACTION2B4 - 115

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