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- PDB-6hut: GFP8 - a stabilized variant of cycle-3 GFP -

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Basic information

Entry
Database: PDB / ID: 6hut
TitleGFP8 - a stabilized variant of cycle-3 GFP
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / green fluorescent protein / cycle-3
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 / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å
AuthorsPetek, M. / Rangel Pereira, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M011194/1 United Kingdom
CitationJournal: To Be Published
Title: GFP8 - a stabilized variant of cycle-3 GFP
Authors: Petek, M. / Rangel Pereira, M.
History
DepositionOct 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)28,4051
Polymers28,4051
Non-polymers00
Water3,801211
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.160, 63.370, 69.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Green fluorescent protein


Mass: 28405.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: gfp / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A059PIQ0, UniProt: P42212*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O
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: 2.04 Å3/Da / Density % sol: 39.8 % / Description: Large cylinder
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 200 mM HEPES, 10% v/v isopropanol, 200 mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.15→35 Å / Num. obs: 58248 / % possible obs: 99.6 % / Redundancy: 7.9 % / CC1/2: 1 / Net I/σ(I): 20.2
Reflection shellResolution: 1.45→1.49 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2865 / CC1/2: 0.2 / Rrim(I) all: 0.634 / % possible all: 95.3

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Processing

Software
NameVersionClassification
AMoRECCP4 7.0phasing
PHENIX1.11.1-2575refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LQT

4lqt


Resolution: 1.29→31.685 Å / Cross valid method: NONE
RfactorNum. reflection% reflection
Rfree0.2034 --
Rwork0.1859 --
obs-58248 99.69 %
Refinement stepCycle: LAST / Resolution: 1.29→31.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1886 0 0 211 2097
LS refinement shellResolution: 1.29→1.3361 Å
RfactorNum. reflection
Rfree0.3342 273
Rwork0.3193 -
obs-5652

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