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- PDB-8yrf: Crystal structure of LmrR with V15 replaced by unnatural amino ac... -

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Basic information

Entry
Database: PDB / ID: 8yrf
TitleCrystal structure of LmrR with V15 replaced by unnatural amino acid 4-amino-L-phenyl-cysteine
ComponentsTranscriptional regulator, PadR-like family
KeywordsDNA BINDING PROTEIN / Inhibitor / Dimeric protein / 4-amino-L-phenyl-cysteine Incorporation / Artificial enzyme
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 / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsZhou, Z. / Huang, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22207043 China
CitationJournal: To Be Published
Title: Crystal structure of LmrR with V15 replaced by unnatural amino acid 4-amino-L-phenyl-cysteine
Authors: Zhou, Z. / Huang, W.
History
DepositionMar 21, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2964
Polymers30,1722
Non-polymers1242
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-12 kcal/mol
Surface area13270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.310, 63.310, 63.920
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Transcriptional regulator, PadR-like family


Mass: 15085.913 Da / Num. of mol.: 2
Mutation: valine 15 replaced with S-(4-Aminophenyl)cysteine(A1D64)
Source method: isolated from a genetically manipulated source
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.45 Å3/Da / Density % sol: 49.75 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.3 M Magnesium nitrate, 0.1 M Tris-HCl, pH 8.0, 20%(w/v) PEG 2000 and 2% (w/v) MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54178 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Feb 27, 2024 / Details: multilayer
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.66→41.65 Å / Num. obs: 8266 / % possible obs: 99.9 % / Redundancy: 4.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.036 / Net I/σ(I): 15.7
Reflection shellResolution: 2.66→2.79 Å / Rmerge(I) obs: 0.597 / Num. unique obs: 1104 / Rpim(I) all: 0.321 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX5.8.0267refinement
ADDREFdata reduction
SCALAdata scaling
ACORNphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.66→41.65 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.902 / SU B: 15.673 / SU ML: 0.322 / Cross valid method: THROUGHOUT / ESU R: 1.049 / ESU R Free: 0.356 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27441 392 4.8 %RANDOM
Rwork0.22701 ---
obs0.22942 7855 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20.27 Å2-0 Å2
2--0.53 Å2-0 Å2
3----1.73 Å2
Refinement stepCycle: 1 / Resolution: 2.66→41.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1796 0 8 5 1809
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191830
X-RAY DIFFRACTIONr_bond_other_d0.0010.021744
X-RAY DIFFRACTIONr_angle_refined_deg1.2521.9742450
X-RAY DIFFRACTIONr_angle_other_deg0.78234002
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4175212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.39124.89898
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.96215350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2061514
X-RAY DIFFRACTIONr_chiral_restr0.0730.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022078
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02440
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.9455.983864
X-RAY DIFFRACTIONr_mcbond_other3.8795.978863
X-RAY DIFFRACTIONr_mcangle_it6.2448.9441080
X-RAY DIFFRACTIONr_mcangle_other6.2478.9541081
X-RAY DIFFRACTIONr_scbond_it3.9196.373966
X-RAY DIFFRACTIONr_scbond_other3.9186.373966
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3139.3391371
X-RAY DIFFRACTIONr_long_range_B_refined9.06567.1322095
X-RAY DIFFRACTIONr_long_range_B_other9.06567.1332096
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2973 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.66→2.727 Å
RfactorNum. reflection% reflection
Rfree0.414 41 -
Rwork0.32 579 -
obs--98.88 %

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