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- PDB-8dpd: superfolder GFP Tyr74pCNPhe mutant -

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Basic information

Entry
Database: PDB / ID: 8dpd
Titlesuperfolder GFP Tyr74pCNPhe mutant
ComponentsSuperfolder green fluorescent protein
KeywordsFLUORESCENT PROTEIN / unnatural amino acid / cyanophenylalanine
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / CARBON DIOXIDE / DI(HYDROXYETHYL)ETHER / 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. / Papoutsis, B. / Piacentini, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1847937 United States
CitationJournal: To Be Published
Title: Superfolder GFP Tyr74pCNPhe mutant
Authors: Phillips-Piro, C.M. / Papoutsis, B. / Piacentini, J.
History
DepositionJul 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 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: Superfolder green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,40311
Polymers26,9071
Non-polymers49610
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.222, 47.222, 346.153
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Superfolder green fluorescent protein


Mass: 26907.336 Da / Num. of mol.: 1
Mutation: S30R, Y39N, F64L, Q80R, F99S, N105T, Y145F, M153T, V163A, I171V, A206V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / Strain (production host): NEB 10 beta / References: UniProt: P42212

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Non-polymers , 5 types, 237 molecules

#2: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.07 Å3/Da / Density % sol: 40.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium chloride, 0.1 M Tris-HCl pH 8.5, 25% PEG 3350

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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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.51→19.9 Å / Num. obs: 37289 / % possible obs: 99.2 % / Redundancy: 8.3 % / Biso Wilson estimate: 23.78 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.6
Reflection shellResolution: 1.51→1.55 Å / Mean I/σ(I) obs: 7.7 / Num. unique obs: 1762 / CC1/2: 0.572

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B3P

2b3p


Resolution: 1.51→19.9 Å / SU ML: 0.2107 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3979
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2518 2000 5.37 %
Rwork0.208 35276 -
obs0.2103 37279 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.97 Å2
Refinement stepCycle: LAST / Resolution: 1.51→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1820 0 30 227 2077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01461994
X-RAY DIFFRACTIONf_angle_d1.52692700
X-RAY DIFFRACTIONf_chiral_restr0.0796288
X-RAY DIFFRACTIONf_plane_restr0.0121358
X-RAY DIFFRACTIONf_dihedral_angle_d11.9307279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.550.35221360.35642400X-RAY DIFFRACTION97.31
1.55-1.590.34181400.31682469X-RAY DIFFRACTION99.77
1.59-1.640.27951420.3122503X-RAY DIFFRACTION99.7
1.64-1.690.36681410.30142489X-RAY DIFFRACTION100
1.69-1.750.39681410.32475X-RAY DIFFRACTION99.92
1.75-1.820.3391410.2912498X-RAY DIFFRACTION99.32
1.82-1.90.34361400.26032476X-RAY DIFFRACTION99.89
1.9-20.29771420.25782510X-RAY DIFFRACTION99.7
2-2.130.30131430.24352518X-RAY DIFFRACTION99.51
2.13-2.290.27971430.22682525X-RAY DIFFRACTION99.44
2.29-2.520.26031440.21122523X-RAY DIFFRACTION98.34
2.52-2.880.24981450.20382555X-RAY DIFFRACTION97.97
2.89-3.630.21091470.17132609X-RAY DIFFRACTION97.56
3.63-19.90.20171550.16292726X-RAY DIFFRACTION94.55

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