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- PDB-9h9w: Crystal structure of metal-free LmrR_V15Bpy in an open state -

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Basic information

Entry
Database: PDB / ID: 9h9w
TitleCrystal structure of metal-free LmrR_V15Bpy in an open 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: 2.26 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)30,5463
Polymers30,2642
Non-polymers2821
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-5 kcal/mol
Surface area12390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.219, 34.955, 66.450
Angle α, β, γ (deg.)90.00, 97.05, 90.00
Int Tables number5
Space group name H-MC121

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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: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C11H26N2O6 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 1.98 Å3/Da / Density % sol: 38.02 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: sodium acetate, 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: 2.26→51.72 Å / Num. obs: 9720 / % possible obs: 85.1 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.026 / Rrim(I) all: 0.054 / Χ2: 0.87 / Net I/σ(I): 13.1 / Num. measured all: 33732
Reflection shellResolution: 2.26→2.33 Å / % possible obs: 49.6 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.584 / Num. measured all: 1054 / Num. unique obs: 509 / CC1/2: 0.554 / Rpim(I) all: 0.455 / Rrim(I) all: 0.744 / Χ2: 1 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.21.1_5286refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→51.72 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 41.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.298 489 5.04 %
Rwork0.2263 --
obs0.2299 9708 84.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.26→51.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1727 0 19 3 1749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091780
X-RAY DIFFRACTIONf_angle_d0.9852387
X-RAY DIFFRACTIONf_dihedral_angle_d14.587688
X-RAY DIFFRACTIONf_chiral_restr0.045251
X-RAY DIFFRACTIONf_plane_restr0.007300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.580.35561340.29932386X-RAY DIFFRACTION67
2.58-3.260.40481830.31013387X-RAY DIFFRACTION94
3.26-51.720.26421720.19623446X-RAY DIFFRACTION93
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)
19.8412-1.5989-4.59332.8922.47359.18830.0226-0.55460.18220.4821-0.0350.19360.1383-0.4259-0.0340.34720.0286-0.03860.42890.01580.563512.96143.003412.9197
29.31092.9550.68676.27391.21787.9210.23470.27840.2421-0.2713-0.0534-0.0733-0.3391-0.6784-0.19410.33950.03170.01450.27010.01060.397215.46774.22442.3452
34.78270.588-4.15561.1939-0.64844.8084-0.076-0.6879-0.35840.3033-0.24-0.33720.33740.50960.39490.5534-0.0297-0.00650.3708-0.01530.671518.777-5.645713.453
46.9707-5.0567-2.48849.32390.98594.62120.54050.06240.24690.0441-0.2281-0.37910.134-1.0332-0.05560.55580.0229-0.10550.7554-0.11720.460513.06011.216728.1969
52.91260.89490.51257.01841.07154.80630.1199-0.3093-0.5290.6264-0.2413-0.87020.8655-0.5523-0.04131.15620.17-0.15590.9370.04270.584111.3094-2.946540.6242
63.5177-2.64610.26943.63081.50632.5795-0.2519-0.99230.69610.1937-0.00230.0521-0.4979-1.05590.27360.88270.2737-0.19630.9242-0.17390.729.467211.264438.9792
76.7442-3.6347-0.93779.7873.21194.5336-0.856-0.2312-0.47490.66660.17570.98490.457-0.6550.98330.4176-0.09940.07680.73030.03040.55012.99510.605214.7781
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 59 )
3X-RAY DIFFRACTION3chain 'A' and (resid 60 through 109 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 23 )
5X-RAY DIFFRACTION5chain 'B' and (resid 24 through 46 )
6X-RAY DIFFRACTION6chain 'B' and (resid 47 through 82 )
7X-RAY DIFFRACTION7chain 'B' and (resid 83 through 112 )

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