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- PDB-9h9x: Crystal structure of metal-free LmrR_V15Bpy in a closed state -

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Basic information

Entry
Database: PDB / ID: 9h9x
TitleCrystal structure of metal-free LmrR_V15Bpy in a closed state
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 / metal ion binding / 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: 2.12 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

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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)30,2642
Polymers30,2642
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-19 kcal/mol
Surface area11270 Å2
Unit cell
Length a, b, c (Å)47.802, 48.282, 91.632
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: 15132.048 Da / Num. of mol.: 2 / Mutation: Val15 replaced by (2,2'-bipyridin-5-yl)alanine
Source method: isolated from a genetically manipulated source
Details: LmrR with residue Val15 replaced by (2,2'-bipyridin-5-yl)alanine and carrying a C-terminal strep-tag
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.: 9 / 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

Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: MES, sodium sulfate, 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: Apr 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 2.12→47.8 Å / Num. obs: 12526 / % possible obs: 99.5 % / Redundancy: 11.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.03 / Rrim(I) all: 0.102 / Χ2: 1.01 / Net I/σ(I): 13.5 / Num. measured all: 138861
Reflection shellResolution: 2.12→2.18 Å / % possible obs: 96 % / Redundancy: 9.8 % / Rmerge(I) obs: 2.228 / Num. measured all: 9524 / Num. unique obs: 976 / CC1/2: 0.459 / Rpim(I) all: 0.739 / Rrim(I) all: 2.353 / Χ2: 0.99 / Net I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0425refinement
PHENIX1.21.1_5286refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→42.72 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 40 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3097 628 5.03 %
Rwork0.2397 --
obs0.2431 12479 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.12→42.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1759 0 0 9 1768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161788
X-RAY DIFFRACTIONf_angle_d1.4692399
X-RAY DIFFRACTIONf_dihedral_angle_d14.09687
X-RAY DIFFRACTIONf_chiral_restr0.072254
X-RAY DIFFRACTIONf_plane_restr0.013306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.330.39891450.32222864X-RAY DIFFRACTION98
2.33-2.670.37051670.28722915X-RAY DIFFRACTION99
2.67-3.360.29621430.27362979X-RAY DIFFRACTION100
3.37-42.720.29331730.2113093X-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)
10.87561.13421.09846.09390.22126.12610.03270.03380.1553-0.2418-0.01420.12930.4243-0.4174-0.11640.2913-0.0197-0.03940.3701-0.0980.3781-20.0191-9.3274-16.1238
27.42614.75731.30087.4891.01334.24230.2993-0.6434-0.90570.7545-0.1315-0.88650.7042-0.1854-0.17030.54440.0644-0.01690.45450.0160.5831-22.3695-22.1534-9.9693
33.59471.0653-0.65053.2889-1.27075.3841-0.39510.41980.38120.69590.3925-0.49750.0365-0.70950.18110.5584-0.04730.03440.6347-0.1050.6029-18.11493.9789-5.7612
45.81042.84960.64867.2861-0.74353.26190.61570.1187-0.27820.0325-0.65180.12110.1810.613-0.14710.4055-0.0022-0.10850.4569-0.19930.3705-8.71651.8706-8.3678
57.80933.6652.02452.6614-0.42582.5211-0.20310.0436-0.7102-0.03570.1176-0.36210.2820.11270.12580.39440.0247-0.01160.3606-0.09720.50050.311211.3333-6.7293
62.75443.19552.08825.96391.38252.18430.16590.75840.6427-0.39310.2894-0.2595-0.56990.6493-0.08880.54280.0027-0.00780.6057-0.11890.3942-15.17261.5163-19.0066
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 46 )
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 81 )
3X-RAY DIFFRACTION3chain 'A' and (resid 82 through 111 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 23 )
5X-RAY DIFFRACTION5chain 'B' and (resid 24 through 82 )
6X-RAY DIFFRACTION6chain 'B' and (resid 83 through 109 )

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