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- PDB-9h9y: Crystal structure of metal-free LmrR_V15Bpy variant BVS in a clos... -

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Basic information

Entry
Database: PDB / ID: 9h9y
TitleCrystal structure of metal-free LmrR_V15Bpy variant BVS in a closed state
ComponentsTranscriptional regulator, PadR-like family
KeywordsMETAL BINDING PROTEIN / artificial metalloenzyme / unnatural amino acid / bipyridine / copper-binding / LmrR
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: 1.5 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


Theoretical massNumber of molelcules
Total (without water)15,1001
Polymers15,1001
Non-polymers00
Water79344
1
A: Transcriptional regulator, PadR-like family

A: Transcriptional regulator, PadR-like family


Theoretical massNumber of molelcules
Total (without water)30,2002
Polymers30,2002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Buried area4630 Å2
ΔGint-12 kcal/mol
Surface area10680 Å2
Unit cell
Length a, b, c (Å)35.039, 35.039, 166.834
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Transcriptional regulator, PadR-like family


Mass: 15100.005 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 1.7 Å3/Da / Density % sol: 27.46 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: sodium nitrate, Bis-Tris propane, 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: 1.5→34.29 Å / Num. obs: 17381 / % possible obs: 98.6 % / Redundancy: 23.8 % / CC1/2: 1 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.013 / Rrim(I) all: 0.064 / Χ2: 0.98 / Net I/σ(I): 21.3 / Num. measured all: 414448
Reflection shellResolution: 1.5→1.53 Å / % possible obs: 95.5 % / Redundancy: 21.3 % / Rmerge(I) obs: 3.178 / Num. measured all: 17282 / Num. unique obs: 813 / CC1/2: 0.524 / Rpim(I) all: 0.692 / Rrim(I) all: 3.256 / Χ2: 0.95 / Net I/σ(I) obs: 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: 1.5→34.29 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2823 896 5.17 %
Rwork0.208 --
obs0.2113 17337 97.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→34.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms839 0 0 44 883
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01881
X-RAY DIFFRACTIONf_angle_d0.9831188
X-RAY DIFFRACTIONf_dihedral_angle_d13.099345
X-RAY DIFFRACTIONf_chiral_restr0.046126
X-RAY DIFFRACTIONf_plane_restr0.011150
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.590.29691520.29212611X-RAY DIFFRACTION96
1.59-1.720.32781550.26822606X-RAY DIFFRACTION97
1.72-1.890.24821550.24562674X-RAY DIFFRACTION98
1.89-2.160.31791510.21572734X-RAY DIFFRACTION98
2.16-2.730.25671440.21552787X-RAY DIFFRACTION99
2.73-34.290.28421390.19463029X-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)
10.37780.25230.48610.0210.23890.5002-0.0508-0.0493-0.11260.04770.24380.04540.2784-0.0525-0.00050.30850.0177-0.06720.356-0.00330.318119.516-15.0186-6.5798
20.36340.49020.24740.55790.43940.644-0.11570.4563-0.2524-0.31920.069-0.2651-0.13050.47750.00040.22790.002-0.01240.37420.02260.400223.9391-13.6209-18.2672
30.11520.03930.04980.14750.06720.1395-0.09970.1285-0.0916-0.14360.14430.25990.10680.20150.00030.2531-0.0126-0.03260.2953-0.00910.324810.7665-18.1388-14.487
40.2556-0.47840.33450.4440.01790.2276-0.02960.0407-0.0729-0.10570.05410.15410.0320.27470.00010.290.0118-0.08420.3077-0.01670.31738.5234-9.4915-21.2576
5-0.00570.31540.81920.2673-0.27290.1281-0.2301-0.19820.65560.0881-0.1941-0.1096-0.3252-0.35470.00020.40050.02-0.02960.38790.02320.3718.7055-5.47571.1705
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 23 )
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 46 )
3X-RAY DIFFRACTION3chain 'A' and (resid 47 through 59 )
4X-RAY DIFFRACTION4chain 'A' and (resid 60 through 82 )
5X-RAY DIFFRACTION5chain 'A' and (resid 83 through 107 )

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