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- PDB-6efr: Crystal Structure of iNicSnFR 1.0 -

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Basic information

Entry
Database: PDB / ID: 6efr
TitleCrystal Structure of iNicSnFR 1.0
ComponentsiNicSnFR 1.0, a genetically encoded nicotine biosensor,Green fluorescent protein
KeywordsCHOLINE-BINDING PROTEIN / periplasmic binding protein / green fluorescent protein
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Green fluorescent protein
Function and homology information
Biological speciesThermoanaerobacter sp. X513 (bacteria)
Aequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
Model detailsBiosensor for nicotine
AuthorsShivange, A.V. / Borden, P.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)DA037161 United States
CitationJournal: J.Gen.Physiol. / Year: 2019
Title: Nicotinic Drugs in the Endoplasmic Reticulum: Beginning the Inside-out Pathway of Addiction and Therapy
Authors: Shivange, A.V. / Borden, P.M. / Muthusamy, A.K. / Nichols, A.L. / Bera, K. / Bao, H. / Bishara, I. / Jeon, J. / Mulcahy, M.J. / Kim, C.H. / Dougherty, D.A. / Chapman, E.R. / Marvin, J.S. / ...Authors: Shivange, A.V. / Borden, P.M. / Muthusamy, A.K. / Nichols, A.L. / Bera, K. / Bao, H. / Bishara, I. / Jeon, J. / Mulcahy, M.J. / Kim, C.H. / Dougherty, D.A. / Chapman, E.R. / Marvin, J.S. / Looger, L.L. / Lester, H.A.
History
DepositionAug 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: iNicSnFR 1.0, a genetically encoded nicotine biosensor,Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)58,4721
Polymers58,4721
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The assembly presents as a monomer by gel filtration.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.610, 95.640, 151.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein iNicSnFR 1.0, a genetically encoded nicotine biosensor,Green fluorescent protein


Mass: 58472.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter sp. X513 (bacteria), (gene. exp.) Aequorea victoria (jellyfish)
Plasmid: pHHM / Gene: GFP / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 6mM nicotine, 50mM MgCl2, 10mM HEPES, 30% PEG 550

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 1, 2015
RadiationMonochromator: Double crystal Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.4→80.85 Å / Num. obs: 23162 / % possible obs: 99.07 % / Redundancy: 14 % / Biso Wilson estimate: 36.65 Å2 / CC1/2: 0.924 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.059 / Rrim(I) all: 0.161 / Net I/σ(I): 47.79
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 14.1 % / Num. unique obs: 46891 / CC1/2: 0.86 / Rpim(I) all: 0.457 / Rrim(I) all: 1.245 / % possible all: 98.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBid 3R6U

3r6u


Resolution: 2.4→61.64 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.67 / Details: Refined using Refmac (initial) and Phenix (final)
RfactorNum. reflection% reflection
Rfree0.2501 1178 5.09 %
Rwork0.1879 --
obs0.1912 23132 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 155.69 Å2 / Biso mean: 45.0672 Å2 / Biso min: 14.59 Å2
Refinement stepCycle: final / Resolution: 2.4→61.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4011 0 0 31 4042
Biso mean---42.6 -
Num. residues----504
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4001-2.50930.35351290.227927072836
2.5093-2.64160.2781340.211527142848
2.6416-2.80710.31251500.2126992849
2.8071-3.02380.30431520.209227092861
3.0238-3.32810.22931540.197427082862
3.3281-3.80970.23841640.186127442908
3.8097-4.79980.20741580.153727702928
4.7998-75.93290.25031370.189429033040
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)
10.26010.1686-0.12630.1971-0.0020.2466-0.2278-0.2820.02520.15640.0841-0.0572-0.0649-0.0256-0.00010.30020.05070.00280.29930.06330.27094.171123.512228.8924
21.4119-0.3987-0.06850.6050.23390.76940.0520.08090.03130.0146-0.04530.06390.0047-0.0691-0.00010.1913-0.02190.00480.19890.02970.145416.919396.447357.2143
30.1915-0.14260.00360.2001-0.150.215-0.00610.13310.2368-0.11790.03210.1498-0.0543-0.19990.00090.40730.0150.03760.35140.05180.40714.988111.418749.1665
40.3795-0.29930.2621.1366-0.42590.2514-0.07920.0839-0.2707-0.109-0.0143-0.01640.14510.0076-00.31190.03890.0760.26130.02680.40619.1313105.61521.3858
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 71 )A2 - 71
2X-RAY DIFFRACTION2chain 'A' and (resid 72 through 303 )A72 - 303
3X-RAY DIFFRACTION3chain 'A' and (resid 304 through 341 )A304 - 341
4X-RAY DIFFRACTION4chain 'A' and (resid 342 through 522 )A342 - 522

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