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- PDB-9h9z: Crystal structure of Cu(II)-bound LmrR_V15Bpy -

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Basic information

Entry
Database: PDB / ID: 9h9z
TitleCrystal structure of Cu(II)-bound LmrR_V15Bpy
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 / COPPER (II) ION / MALONATE ION / 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: 1.9 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)30,4935
Polymers30,2642
Non-polymers2293
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-31 kcal/mol
Surface area13610 Å2
Unit cell
Length a, b, c (Å)35.496, 53.359, 147.778
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, 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-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 280 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: malonate, imidazole, boric acid, 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: Jul 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 1.9→34.51 Å / Num. obs: 22559 / % possible obs: 98.3 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.03 / Rrim(I) all: 0.076 / Χ2: 1.07 / Net I/σ(I): 13.3 / Num. measured all: 146523
Reflection shellResolution: 1.9→1.94 Å / % possible obs: 96.8 % / Redundancy: 6.5 % / Rmerge(I) obs: 2.315 / Num. measured all: 9231 / Num. unique obs: 1412 / CC1/2: 0.384 / Rpim(I) all: 0.975 / Rrim(I) all: 2.517 / Χ2: 1.25 / Net I/σ(I) obs: 0.9

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.21.1_5286refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→34.51 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 0.33 / Phase error: 29.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2392 2075 4.95 %
Rwork0.202 --
obs0.2039 20960 98.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→34.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1848 0 9 78 1935
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121892
X-RAY DIFFRACTIONf_angle_d1.1622535
X-RAY DIFFRACTIONf_dihedral_angle_d13.308732
X-RAY DIFFRACTIONf_chiral_restr0.062266
X-RAY DIFFRACTIONf_plane_restr0.011326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.46791520.38322586X-RAY DIFFRACTION96
1.94-1.990.36771420.33662606X-RAY DIFFRACTION97
1.99-2.050.29391200.28452703X-RAY DIFFRACTION99
2.05-2.110.31861350.27942564X-RAY DIFFRACTION96
2.11-2.170.28941220.25142726X-RAY DIFFRACTION100
2.18-2.250.27671360.23962604X-RAY DIFFRACTION96
2.25-2.340.30881340.21952713X-RAY DIFFRACTION99
2.34-2.450.27911490.20772635X-RAY DIFFRACTION98
2.45-2.580.26421360.21982636X-RAY DIFFRACTION98
2.58-2.740.27461380.21322656X-RAY DIFFRACTION98
2.74-2.950.24981540.22172693X-RAY DIFFRACTION99
2.95-3.250.19841350.21662663X-RAY DIFFRACTION99
3.25-3.720.23071580.18862654X-RAY DIFFRACTION99
3.72-4.680.19721420.15392692X-RAY DIFFRACTION99
4.69-34.510.21531220.18042714X-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)
10.509-0.22350.46010.8245-0.74430.8127-0.03120.04140.02750.1412-0.0748-0.0495-0.02590.2252-0.00010.2930.03060.01280.37810.05480.3568-7.8973-17.557815.8956
20.32350.27160.16280.3651-0.03460.2548-0.2220.1583-0.166-0.23960.2850.36981.0787-0.3917-0.00010.56130.03090.08150.36760.04320.3973-9.4494-28.07779.099
30.46640.24860.10040.6457-0.80381.3748-0.11590.06490.1905-0.0850.0280.10690.03170.10620.00010.31870.01430.00230.5170.08340.324-7.2496-13.71861.4268
40.0330.0280.13280.4982-0.41460.475-0.28380.2016-0.04580.1721-0.0666-0.2158-0.00940.4335-0.00030.4061-0.0481-0.01690.4780.04160.46593.204-10.384730.3737
50.5335-0.1823-0.37190.09150.15110.2661-0.11160.2636-0.04070.05630.11010.1461-0.06940.00640.00030.381-0.008-0.01080.36410.02980.3914-7.0915-8.410930.7307
60.3606-0.4383-0.2610.74310.38240.5343-0.06-0.11470.22120.31120.1181-0.1504-0.1599-0.03660.00010.4365-0.069-0.03060.35430.00490.412-3.4863-1.324240.8576
70.6047-0.5678-0.48530.48370.43540.36420.0203-0.0655-0.18640.1202-0.1067-0.06250.0083-0.1717-0.00010.4160.00240.03620.3606-0.00830.4091-18.2796-3.350742.0243
80.1001-0.3261-0.00481.163-0.16080.6222-0.0343-0.08510.05980.2481-0.09480.05670.4930.17090.00520.37940.04-0.00510.34710.04610.365-7.3853-21.247228.0412
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 27 )
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 46 )
3X-RAY DIFFRACTION3chain 'A' and (resid 47 through 82 )
4X-RAY DIFFRACTION4chain 'A' and (resid 83 through 115 )
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 23 )
6X-RAY DIFFRACTION6chain 'B' and (resid 24 through 46 )
7X-RAY DIFFRACTION7chain 'B' and (resid 47 through 75 )
8X-RAY DIFFRACTION8chain 'B' and (resid 76 through 114 )

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