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- PDB-1jby: CRYSTAL STRUCTURE ANALYSIS OF A DUAL-WAVELENGTH EMISSION GREEN FL... -

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Basic information

Entry
Database: PDB / ID: 1jby
TitleCRYSTAL STRUCTURE ANALYSIS OF A DUAL-WAVELENGTH EMISSION GREEN FLUORESCENT PROTEIN VARIANT AT LOW PH
ComponentsGREEN FLUORESCENT PROTEIN
KeywordsLUMINESCENT PROTEIN / Beta Barrel / Chromophore
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHanson, G.T. / McAnaney, T.B. / Park, E.S. / Rendell, M.E.P. / Yarbrough, D.K. / Chu, S. / Xi, L. / Boxer, S.G. / Montrose, M.H. / Remington, S.J.
CitationJournal: Biochemistry / Year: 2002
Title: Green Fluorescent Protein Variants as Ratiometric Dual Emission pH Sensors. 1. Structural Characterization and Preliminary Application.
Authors: Hanson, G.T. / McAnaney, T.B. / Park, E.S. / Rendell, M.E.P. / Yarbrough, D.K. / Chu, S. / Xi, L. / Boxer, S.G. / Montrose, M.H. / Remington, S.J.
History
DepositionJun 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)26,8661
Polymers26,8661
Non-polymers00
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.953, 62.244, 67.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GREEN FLUORESCENT PROTEIN / Dual Emission Green Fluorescent Protein / deGFP1


Mass: 26866.326 Da / Num. of mol.: 1 / Mutation: S65T,Q80R,H148G,T203C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Plasmid: pRSETb / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUES 65, 66, AND 67 ARE NOT PRESENT IN THE ENTRY AND ARE INSTEAD REPLACED WITH CRO 66

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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: 1.98 Å3/Da / Density % sol: 37.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 1550, citrate, ammonium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
pH: 7.9
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
148 mg/mlprotein1drop
220 mMHEPES1droppH7.9
3100 mMcitrate-NaOH1reservoirpH4.5
4100 mMammonium acetate1reservoir
514 %PEG15501reservoirpH5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 19, 2000 / Details: mirrors
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→19.5 Å / Num. all: 18903 / Num. obs: 18903 / % possible obs: 93 % / Redundancy: 4.4 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 6.4
Reflection shellResolution: 1.8→1.89 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2522 / % possible all: 87.2
Reflection
*PLUS
Num. measured all: 83420
Reflection shell
*PLUS
% possible obs: 87.2 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
TNTrefinement
CCP4(SCALA)data scaling
TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EMA

1ema


Resolution: 1.8→19.5 Å / Stereochemistry target values: ENGH & HUBER /
RfactorNum. reflection
Rwork0.194 -
obs-18853
Refinement stepCycle: LAST / Resolution: 1.8→19.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1743 0 0 114 1857
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.076
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_dihedral_angle_d19.625
LS refinement shellResolution: 1.8→1.89 Å
RfactorNum. reflection% reflection
Rwork0.32 --
obs-1695 87.2 %
Refinement
*PLUS
Rfactor all: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.1
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg19.625

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