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- PDB-9c74: superfolder Green Fluorescent Protein with meta-nitro-tyrosine in... -

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Basic information

Entry
Database: PDB / ID: 9c74
Titlesuperfolder Green Fluorescent Protein with meta-nitro-tyrosine incorporated at position 66
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / nitrotyrosine / GFP / sfGFP / UAA / ncAA
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 speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsPhillips-Piro, C.M. / Broughton, D.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1847937 United States
CitationJournal: Rsc Adv / Year: 2024
Title: Modulating the pH dependent photophysical properties of green fluorescent protein.
Authors: Broughton, D.P. / Holod, C.G. / Camilo-Contreras, A. / Harris, D.R. / Brewer, S.H. / Phillips-Piro, C.M.
History
DepositionJun 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1274
Polymers27,0581
Non-polymers693
Water6,251347
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.809, 37.967, 68.464
Angle α, β, γ (deg.)90.000, 112.733, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-411-

HOH

21A-576-

HOH

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Components

#1: Protein Green fluorescent protein


Mass: 27058.439 Da / Num. of mol.: 1 / Mutation: Y66mNO2Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: gfp
Production host: Escherichia coli str. K-12 substr. DH10B (bacteria)
References: UniProt: A0A059PIQ0
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 2.03 Å3/Da / Density % sol: 39.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1% tryptone, 0.001 M NaN3, 0.05 M Hepes pH 7.0, 20% w/v PEG350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.51→63.15 Å / Num. obs: 55986 / % possible obs: 97.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 21.55 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.4
Reflection shellResolution: 1.51→1.53 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1508 / CC1/2: 0.869 / % possible all: 90.1

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
XDSdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→63.15 Å / SU ML: 0.1906 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 23.7626
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2197 3362 6.01 %
Rwork0.1699 52603 -
obs0.1729 55965 83.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.99 Å2
Refinement stepCycle: LAST / Resolution: 1.51→63.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1804 0 3 347 2154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011866
X-RAY DIFFRACTIONf_angle_d1.16512528
X-RAY DIFFRACTIONf_chiral_restr0.074275
X-RAY DIFFRACTIONf_plane_restr0.0124331
X-RAY DIFFRACTIONf_dihedral_angle_d15.3189700
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.530.32081200.27051920X-RAY DIFFRACTION72.68
1.53-1.550.30971410.25772136X-RAY DIFFRACTION81.91
1.55-1.580.31151440.24642165X-RAY DIFFRACTION83.03
1.58-1.60.27051300.23462176X-RAY DIFFRACTION81.8
1.6-1.630.2741340.23642168X-RAY DIFFRACTION82.36
1.63-1.660.30021330.23682128X-RAY DIFFRACTION80.01
1.66-1.690.2781400.22082177X-RAY DIFFRACTION84.53
1.69-1.730.27391450.20512276X-RAY DIFFRACTION84.03
1.73-1.760.21681410.20892171X-RAY DIFFRACTION84.53
1.76-1.80.2511420.21442256X-RAY DIFFRACTION84.98
1.8-1.850.27071420.22082233X-RAY DIFFRACTION84.58
1.85-1.90.2891420.2152265X-RAY DIFFRACTION85.05
1.9-1.960.25961430.22192207X-RAY DIFFRACTION84.72
1.96-2.020.32441460.20212211X-RAY DIFFRACTION84.18
2.02-2.090.2661420.19522217X-RAY DIFFRACTION84.07
2.09-2.170.23541430.19272236X-RAY DIFFRACTION85.36
2.17-2.270.24051340.18042135X-RAY DIFFRACTION80.95
2.27-2.390.24841450.16752189X-RAY DIFFRACTION83.51
2.39-2.540.19841400.16742269X-RAY DIFFRACTION85.58
2.54-2.740.20721430.17052227X-RAY DIFFRACTION84.22
2.74-3.020.20141390.16142192X-RAY DIFFRACTION83.61
3.02-3.450.19551470.14622168X-RAY DIFFRACTION82.74
3.45-4.350.20311340.12942181X-RAY DIFFRACTION82.68
4.35-63.150.1611520.13932300X-RAY DIFFRACTION87.01

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