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- PDB-9iij: Engineered LmrR with V15 replaced by unnatural amino acid 4-amino... -

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Basic information

Entry
Database: PDB / ID: 9iij
TitleEngineered LmrR with V15 replaced by unnatural amino acid 4-amino-L-phenyl-cysteine
ComponentsTranscriptional regulator, PadR-like family
KeywordsTRANSCRIPTION / LmrR / Artificial Enzymes / Unnatural Amino Acid
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: 2.7 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: Engineered LmrR with V15 replaced by unnatural amino acid 4-amino-L-phenyl-cysteine
Authors: Zhou, Z. / Huang, W.
History
DepositionJun 20, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1422
Polymers14,0801
Non-polymers621
Water00
1
A: Transcriptional regulator, PadR-like family
hetero molecules

A: Transcriptional regulator, PadR-like family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2844
Polymers28,1602
Non-polymers1242
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565x,x-y+1,-z1
Buried area3300 Å2
ΔGint-5 kcal/mol
Surface area13380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.620, 70.620, 61.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

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Components

#1: Protein Transcriptional regulator, PadR-like family


Mass: 14079.756 Da / Num. of mol.: 1
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.: 1 / Source method: obtained synthetically / Formula: C2H6O2
Has ligand of interestN
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: 2.92 Å3/Da / Density % sol: 57.81 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEGRX2 containing 1.8M Ammonium sulfate, 0.1M Bis-Tris, pH 6.5 and 2% (v/v) PEG 550

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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: Jan 12, 2024 / Details: multilayer
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.7→43.34 Å / Num. obs: 4944 / % possible obs: 100 % / Redundancy: 8.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.035 / Net I/σ(I): 17.7
Reflection shellResolution: 2.7→2.83 Å / Rmerge(I) obs: 1.094 / Num. unique obs: 663 / Rpim(I) all: 0.411 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→43.34 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.879 / SU B: 18.681 / SU ML: 0.362 / Cross valid method: THROUGHOUT / ESU R: 0.613 / ESU R Free: 0.345 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28605 208 4.2 %RANDOM
Rwork0.24175 ---
obs0.2439 4719 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: 66.893 Å2
Baniso -1Baniso -2Baniso -3
1--1.26 Å2-0.63 Å2-0 Å2
2---1.26 Å20 Å2
3---4.1 Å2
Refinement stepCycle: 1 / Resolution: 2.7→43.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms909 0 4 0 913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.019925
X-RAY DIFFRACTIONr_bond_other_d0.0010.02888
X-RAY DIFFRACTIONr_angle_refined_deg0.9371.9811240
X-RAY DIFFRACTIONr_angle_other_deg0.71232038
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8435107
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.54324.850
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.14815179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.085158
X-RAY DIFFRACTIONr_chiral_restr0.0550.2131
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021049
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02219
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_it2.6366.617436
X-RAY DIFFRACTIONr_mcbond_other2.5876.606435
X-RAY DIFFRACTIONr_mcangle_it4.4699.894545
X-RAY DIFFRACTIONr_mcangle_other4.4719.909546
X-RAY DIFFRACTIONr_scbond_it2.0366.74489
X-RAY DIFFRACTIONr_scbond_other2.0316.74489
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5989.988696
X-RAY DIFFRACTIONr_long_range_B_refined5.97174.1521055
X-RAY DIFFRACTIONr_long_range_B_other5.96874.1351056
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.701→2.771 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.744 14 -
Rwork0.343 345 -
obs--100 %

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