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- PDB-9jti: X-ray structure of NeIle indicator complexed with isoleucine -

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Basic information

Entry
Database: PDB / ID: 9jti
TitleX-ray structure of NeIle indicator complexed with isoleucine
ComponentsNeIle,Leu/Ile/Val-binding protein
KeywordsFLUORESCENT PROTEIN / chimeric protein / branched-chain amino acids indicator
Function / homology
Function and homology information


branched-chain amino acid transport / isoleucine transport / valine transport / L-leucine transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space / membrane
Similarity search - Function
Leu/Ile/Val-binding protein / Leucine-binding protein domain / Periplasmic binding protein / Periplasmic binding protein-like I
Similarity search - Domain/homology
ISOLEUCINE / Leu/Ile/Val-binding protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsSamygina, V.R. / Subach, O.M. / Vlaskina, A.V. / Dronova, E.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
DepositionOct 4, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2025Group: Structure summary / Category: struct / Item: _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)64,9646
Polymers64,5211
Non-polymers4435
Water10,088560
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-12 kcal/mol
Surface area24790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.100, 69.200, 80.500
Angle α, β, γ (deg.)90.000, 111.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 64521.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GYG = CR2 (chromophore)
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Escherichia coli O157:H7 (bacteria)
Gene: livJ, b3460, JW3425 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AD96
#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.: 3 / 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: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 560 / 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: 2.47 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, 0.2M Sodium Acetate, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.62→75.55 Å / Num. obs: 88962 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.99 / Net I/σ(I): 7.5
Reflection shellResolution: 1.62→1.65 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 6547 / CC1/2: 0.56

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→75.55 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.714 / SU ML: 0.057 / Cross valid method: FREE R-VALUE / ESU R: 0.079 / ESU R Free: 0.078
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1837 3978 5.001 %
Rwork0.1575 75559 -
all0.159 --
obs-79537 99.953 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.545 Å2
Baniso -1Baniso -2Baniso -3
1-0.274 Å20 Å2-0.129 Å2
2--0.119 Å20 Å2
3----0.226 Å2
Refinement stepCycle: LAST / Resolution: 1.62→75.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4370 0 47 560 4977
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134624
X-RAY DIFFRACTIONr_bond_other_d0.0030.0174206
X-RAY DIFFRACTIONr_angle_refined_deg1.7311.656274
X-RAY DIFFRACTIONr_angle_other_deg1.3381.5849798
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6495594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02823.553228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.18415757
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4131519
X-RAY DIFFRACTIONr_chiral_restr0.0790.2593
X-RAY DIFFRACTIONr_chiral_restr_other0.2340.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025269
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02952
X-RAY DIFFRACTIONr_nbd_refined0.2320.2627
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.23158
X-RAY DIFFRACTIONr_nbtor_refined0.1510.22005
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21568
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2254
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2420.27
X-RAY DIFFRACTIONr_nbd_other0.1940.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2060.233
X-RAY DIFFRACTIONr_mcbond_it1.6451.6842325
X-RAY DIFFRACTIONr_mcbond_other1.6461.6842324
X-RAY DIFFRACTIONr_mcangle_it2.6452.5152912
X-RAY DIFFRACTIONr_mcangle_other2.6452.5142913
X-RAY DIFFRACTIONr_scbond_it2.6671.9812299
X-RAY DIFFRACTIONr_scbond_other2.6661.9822300
X-RAY DIFFRACTIONr_scangle_it4.1942.8333354
X-RAY DIFFRACTIONr_scangle_other4.1932.8343355
X-RAY DIFFRACTIONr_lrange_it6.59220.8934731
X-RAY DIFFRACTIONr_lrange_other6.207204617
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.6620.2962910.2685540X-RAY DIFFRACTION99.9828
1.662-1.7080.2962870.2465454X-RAY DIFFRACTION99.9826
1.708-1.7570.2482770.2335252X-RAY DIFFRACTION100
1.757-1.8110.2282670.2135144X-RAY DIFFRACTION99.9631
1.811-1.870.2412620.194968X-RAY DIFFRACTION100
1.87-1.9360.2212730.1754750X-RAY DIFFRACTION99.9403
1.936-2.0090.1822240.1594673X-RAY DIFFRACTION99.9796
2.009-2.0910.1872040.154520X-RAY DIFFRACTION99.9788
2.091-2.1840.1662050.1454315X-RAY DIFFRACTION100
2.184-2.2910.1832570.1464033X-RAY DIFFRACTION100
2.291-2.4140.1782020.1393893X-RAY DIFFRACTION99.9756
2.414-2.5610.1672060.1413720X-RAY DIFFRACTION99.9491
2.561-2.7370.1791970.1433428X-RAY DIFFRACTION99.9449
2.737-2.9560.1661700.1463260X-RAY DIFFRACTION100
2.956-3.2380.1711470.1423005X-RAY DIFFRACTION99.9049
3.238-3.6190.1741550.142684X-RAY DIFFRACTION99.8944
3.619-4.1770.1531270.132383X-RAY DIFFRACTION99.9602
4.177-5.1120.1411250.1262034X-RAY DIFFRACTION99.9537
5.112-7.2130.181630.1791596X-RAY DIFFRACTION99.8796
7.213-7.550.182390.17907X-RAY DIFFRACTION98.6444

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