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- PDB-9ha0: Crystal structure of Cu(II)-bound LmrR_V15Bpy variant BVS -

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Basic information

Entry
Database: PDB / ID: 9ha0
TitleCrystal structure of Cu(II)-bound LmrR_V15Bpy variant BVS
ComponentsTranscriptional regulator, PadR-like family
KeywordsMETAL BINDING PROTEIN / artificial metalloenzyme / unnatural amino acid / bipyridine / copper-binding / LmrR / directed evolution
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 / COPPER (II) ION / IMIDAZOLE / 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: 1.75 Å
AuthorsThunnissen, A.M.W.H. / Jiang, R. / Casilli, F. / Aalbers, F. / Roelfes, G.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)885396European Union
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: An Artificial Copper-Michaelase Featuring a Genetically Encoded Bipyridine Ligand for Asymmetric Additions to Nitroalkenes.
Authors: Jiang, R. / Casilli, F. / Thunnissen, A.W.H. / Roelfes, G.
History
DepositionNov 1, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)30,4946
Polymers30,2002
Non-polymers2944
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-16 kcal/mol
Surface area12450 Å2
Unit cell
Length a, b, c (Å)35.395, 54.313, 145.734
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: 15100.005 Da / Num. of mol.: 2
Mutation: Val15 replaced by (2,2'-bipyridin-5-yl)alanine, A92V, F93S
Source method: isolated from a genetically manipulated source
Details: LmrR with residue Val15 replaced by (2,2'-bipyridin-5-yl)alanine, carrying a C-terminal strep-tag and with evolved mutations A92V, F93S
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.32 Å3/Da / Density % sol: 46.96 %
Crystal growTemperature: 280 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: Copper nitrate, imidazole, PEG 8000

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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 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 1.75→43.55 Å / Num. obs: 29303 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.025 / Rrim(I) all: 0.089 / Χ2: 1.01 / Net I/σ(I): 15.2 / Num. measured all: 377849
Reflection shellResolution: 1.75→1.78 Å / % possible obs: 99.8 % / Redundancy: 13.2 % / Rmerge(I) obs: 2.758 / Num. measured all: 20638 / Num. unique obs: 1567 / CC1/2: 0.502 / Rpim(I) all: 0.78 / Rrim(I) all: 2.868 / Χ2: 0.92 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.21.1_5286refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→36.43 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2353 1437 4.92 %
Rwork0.1981 --
obs0.1999 29233 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→36.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1802 0 17 105 1924
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081907
X-RAY DIFFRACTIONf_angle_d0.8712561
X-RAY DIFFRACTIONf_dihedral_angle_d14.337752
X-RAY DIFFRACTIONf_chiral_restr0.045269
X-RAY DIFFRACTIONf_plane_restr0.012326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.810.34221450.31022717X-RAY DIFFRACTION100
1.81-1.890.35591490.30272702X-RAY DIFFRACTION100
1.89-1.970.36641380.27232772X-RAY DIFFRACTION100
1.97-2.070.26271180.22582755X-RAY DIFFRACTION100
2.07-2.20.23731610.21452714X-RAY DIFFRACTION100
2.2-2.370.25991500.21072759X-RAY DIFFRACTION100
2.38-2.610.26221410.20322767X-RAY DIFFRACTION100
2.61-2.990.25541450.20622802X-RAY DIFFRACTION100
2.99-3.770.21781300.18762827X-RAY DIFFRACTION100
3.77-36.430.19811600.17242981X-RAY DIFFRACTION100
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)
17.5012-0.5052-3.374.7223-1.95462.5097-0.5235-0.2631-0.61150.80910.35120.4537-0.0419-0.42140.11330.47230.06110.07710.29570.07590.38067.2657-8.9435-30.5125
28.70050.8663-2.05173.8180.62555.32110.0330.05590.36830.1489-0.08430.53270.0636-0.70550.06630.27450.01650.04730.27960.02920.35623.2849-1.2036-39.408
32.3661.3966-1.343.1885-1.04964.1179-0.02820.15880.0498-0.0692-0.0821-0.0380.101-0.03570.10340.26470.00570.04580.2046-0.00250.307117.0871-2.3292-41.4902
46.18651.7762-4.87453.0105-1.41397.1750.0739-0.0847-0.2160.1691-0.40040.23240.1137-0.55650.30520.3153-0.07010.04020.2942-0.12460.31425.9498-22.8217-26.2997
51.8819-0.3236-1.62990.84190.86456.7498-0.1476-0.20170.0629-0.093-0.009-0.04220.5223-0.07730.14870.3068-0.02180.02650.3153-0.07920.3088.2561-20.6122-14.606
66.0966-2.1395-0.05142.30050.47964.0709-0.0138-0.17270.3964-0.00510.1007-0.05480.0861-0.1134-0.03630.2349-0.0516-0.02890.3713-0.11990.26187.675-13.183-2.3083
70.592-0.00570.5818-0.0315-0.25417.6581-0.0182-0.05080.1189-0.0460.05310.0243-0.2411-0.7488-0.05270.30340.00990.04760.5495-0.01550.4534-1.9603-11.3617-24.1729
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 23 )
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 46 )
3X-RAY DIFFRACTION3chain 'A' and (resid 47 through 82 )
4X-RAY DIFFRACTION4chain 'A' and (resid 83 through 112 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 46 )
6X-RAY DIFFRACTION6chain 'B' and (resid 47 through 76 )
7X-RAY DIFFRACTION7chain 'B' and (resid 77 through 114 )

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