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- PDB-8z0g: Crystal structure of NeIle complexed with isoleucine -

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Basic information

Entry
Database: PDB / ID: 8z0g
TitleCrystal structure of NeIle complexed with isoleucine
ComponentsLeu/Ile/Val-binding protein,Leu/Ile/Val-binding protein,mNeonGreen
KeywordsFLUORESCENT PROTEIN / fluorescent protein based sensor
Function / homologyLeu/Ile/Val-binding protein / Leucine-binding protein domain / Periplasmic binding protein / amino acid transport / Periplasmic binding protein-like I / periplasmic space / ISOLEUCINE / Leu/Ile/Val-binding protein
Function and homology information
Biological speciesEscherichia coli O157:H7 (bacteria)
Branchiostoma lanceolatum (amphioxus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsSamygina, V.R. / Subach, O.M. / Vlaskina, A.V. / Gabdukhakov, A. / Subach, F.V.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: ACS Sens / Year: 2024
Title: NeIle, a Genetically Encoded Indicator for Branched-Chain Amino Acids Based on mNeonGreen Fluorescent Protein and LIVBP Protein.
Authors: Asanova, A.N. / Subach, O.M. / Myachina, S.A. / Evteeva, M.A. / Gunitseva, N.M. / Borisova, A.A. / Patrushev, M.V. / Vlaskina, A.V. / Nikolaeva, A.Y. / Yang, L. / Gabdulkhakov, A. / Dronova, ...Authors: Asanova, A.N. / Subach, O.M. / Myachina, S.A. / Evteeva, M.A. / Gunitseva, N.M. / Borisova, A.A. / Patrushev, M.V. / Vlaskina, A.V. / Nikolaeva, A.Y. / Yang, L. / Gabdulkhakov, A. / Dronova, E. / Samygina, V.R. / Xiao, X. / Zhao, H. / Piatkevich, K.D. / Subach, F.V.
History
DepositionApr 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leu/Ile/Val-binding protein,Leu/Ile/Val-binding protein,mNeonGreen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7644
Polymers64,5051
Non-polymers2593
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint-12 kcal/mol
Surface area23480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.128, 68.153, 79.479
Angle α, β, γ (deg.)90.00, 112.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Leu/Ile/Val-binding protein,Leu/Ile/Val-binding protein,mNeonGreen / LIV-BP


Mass: 64505.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CR2 is mature chromophore (GYG), chimera of fluorescent protein and LIVBP protein
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria), (gene. exp.) Branchiostoma lanceolatum (amphioxus)
Gene: livJ, Z4834, ECs4309, blFP-Y3 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AD98
#2: Chemical ChemComp-ILE / ISOLEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, Sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5416 Å
DetectorType: RIGAKU HyPix-Arc 100 / Detector: PIXEL / Date: Feb 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5416 Å / Relative weight: 1
ReflectionResolution: 2.65→22.16 Å / Num. obs: 18097 / % possible obs: 98.26 % / Redundancy: 3.7 % / CC1/2: 0.92 / Net I/σ(I): 1.5
Reflection shellResolution: 2.65→2.72 Å / Num. unique obs: 1254 / CC1/2: 0.65

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→22.16 Å / Cor.coef. Fo:Fc: 0.88 / Cor.coef. Fo:Fc free: 0.769 / SU B: 17.603 / SU ML: 0.367 / Cross valid method: THROUGHOUT / ESU R Free: 0.426 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30781 903 5 %RANDOM
Rwork0.23502 ---
obs0.2387 17075 98.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.859 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å2-0.57 Å2
2---0.29 Å20 Å2
3----0.07 Å2
Refinement stepCycle: 1 / Resolution: 2.65→22.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4353 0 16 74 4443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0134466
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174182
X-RAY DIFFRACTIONr_angle_refined_deg2.2751.656043
X-RAY DIFFRACTIONr_angle_other_deg1.3421.5889637
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.4995562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.56523.535215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.8815730
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.7911518
X-RAY DIFFRACTIONr_chiral_restr0.0920.2574
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025136
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021016
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_it2.832.9832260
X-RAY DIFFRACTIONr_mcbond_other2.8292.9832259
X-RAY DIFFRACTIONr_mcangle_it4.2344.4662818
X-RAY DIFFRACTIONr_mcangle_other4.2334.4662819
X-RAY DIFFRACTIONr_scbond_it2.9463.1572206
X-RAY DIFFRACTIONr_scbond_other2.9463.1572207
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4334.6383226
X-RAY DIFFRACTIONr_long_range_B_refined6.99334.6434964
X-RAY DIFFRACTIONr_long_range_B_other6.99334.6474964
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 55 -
Rwork0.257 1254 -
obs--97.91 %

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