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- PDB-6dq0: sfGFP D133 mutated to 4-nitro-L-phenylalanine -

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Basic information

Entry
Database: PDB / ID: 6dq0
TitlesfGFP D133 mutated to 4-nitro-L-phenylalanine
Componentssuperfolder green fluorescent protein
KeywordsFLUORESCENT PROTEIN / super folder GFP / 4-nitro-L-phenylalanine / unnatural amino acid
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.048 Å
AuthorsPhillips-Piro, C.M. / Maurici, N. / Lee, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1053946 United States
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Crystal structures of green fluorescent protein with the unnatural amino acid 4-nitro-L-phenylalanine.
Authors: Maurici, N. / Savidge, N. / Lee, B.U. / Brewer, S.H. / Phillips-Piro, C.M.
History
DepositionJun 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 27, 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: superfolder green fluorescent protein
B: superfolder green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2227
Polymers53,9512
Non-polymers2715
Water5,639313
1
A: superfolder green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1855
Polymers26,9751
Non-polymers2094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: superfolder green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0372
Polymers26,9751
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.720, 97.720, 154.872
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein superfolder green fluorescent protein


Mass: 26975.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Production host: Escherichia coli (E. coli) / References: UniProt: P42212*PLUS
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 3.96 Å3/Da / Density % sol: 68.91 % / Description: 400x400x50 um
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Ammonium citrate tribasic pH 7.0, 18% PEG3350; protein at 36 mg/mL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97919 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.048→50 Å / Num. obs: 53525 / % possible obs: 98.5 % / Redundancy: 6.6 % / CC1/2: 0.995 / Net I/σ(I): 21.36
Reflection shellResolution: 2.048→2.09 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 1.56 / Num. unique obs: 2616 / CC1/2: 0.745 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER(in Phenix)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B3P

2b3p


Resolution: 2.048→48.86 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2189 2552 4.77 %
Rwork0.185 --
obs0.1866 53521 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.048→48.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3652 0 17 313 3982
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013787
X-RAY DIFFRACTIONf_angle_d1.0265111
X-RAY DIFFRACTIONf_dihedral_angle_d9.6943133
X-RAY DIFFRACTIONf_chiral_restr0.065553
X-RAY DIFFRACTIONf_plane_restr0.01713
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0476-2.0870.28961310.26192546X-RAY DIFFRACTION89
2.087-2.12960.28641120.25732806X-RAY DIFFRACTION98
2.1296-2.17590.29361410.24162792X-RAY DIFFRACTION98
2.1759-2.22650.28781570.2342775X-RAY DIFFRACTION98
2.2265-2.28220.31191140.23512803X-RAY DIFFRACTION98
2.2822-2.34390.25051490.22742791X-RAY DIFFRACTION98
2.3439-2.41280.26391170.21922832X-RAY DIFFRACTION99
2.4128-2.49070.28381630.21652817X-RAY DIFFRACTION99
2.4907-2.57970.20791250.20552839X-RAY DIFFRACTION99
2.5797-2.6830.22341400.20922814X-RAY DIFFRACTION98
2.683-2.80510.2721570.21162832X-RAY DIFFRACTION99
2.8051-2.9530.26081650.20642803X-RAY DIFFRACTION98
2.953-3.1380.22891460.19482853X-RAY DIFFRACTION99
3.138-3.38020.23371460.18942886X-RAY DIFFRACTION99
3.3802-3.72030.21171500.18182876X-RAY DIFFRACTION100
3.7203-4.25830.19871250.15832923X-RAY DIFFRACTION99
4.2583-5.3640.16711440.13672941X-RAY DIFFRACTION100
5.364-48.87390.17731700.17233040X-RAY DIFFRACTION99

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