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- PDB-1q4d: S65T Q80R T203C Green Fluorescent Protein (GFP) pH 5.5 -

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Basic information

Entry
Database: PDB / ID: 1q4d
TitleS65T Q80R T203C Green Fluorescent Protein (GFP) pH 5.5
ComponentsGreen Fluorescent Protein
KeywordsLUMINESCENT PROTEIN / green fluorescent protein / GFP / fluorophore / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsJain, R.K. / Ranganathan, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Local complexity of amino acid interactions in a protein core.
Authors: Jain, R.K. / Ranganathan, R.
History
DepositionAug 2, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 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 1.4Oct 25, 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 1.6Nov 13, 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)26,9471
Polymers26,9471
Non-polymers00
Water3,405189
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.969, 62.333, 68.554
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


Mass: 26947.422 Da / Num. of mol.: 1 / Mutation: Q80R, S65T, T203C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Plasmid: pRSET-B (Invitrogen) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUE SER A 65 IS MUTATED TO THR A 65. THR A 65, TYR A 66 AND GLY A 67 ARE MODIFIED TO MAKE ...RESIDUE SER A 65 IS MUTATED TO THR A 65. THR A 65, TYR A 66 AND GLY A 67 ARE MODIFIED TO MAKE CHROMOPHORE (CRO A 66). RESIDUE THR A 203 IS MUTATED TO CYS A 203.

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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: 1.94 Å3/Da / Density % sol: 36.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 4000, MgCl2, BME, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 8.5 / PH range high: 8.1
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
122-26 %PEG40001reservoir
250 mM1reservoirMgCl2
310 mM2-mercaptoethanol1reservoir
450 mMHEPES1reservoirpH8.1-8.5
512-15 mg/mlprotein1drop
650 mMHEPES1droppH7.5

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.58→25 Å / Num. all: 30578 / Num. obs: 30578 / % possible obs: 99.9 %
Reflection
*PLUS
Redundancy: 4.7 % / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
% possible obs: 99.4 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EMA

1ema


Resolution: 1.58→25 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2938 -Random
Rwork0.208 ---
obs0.208 30578 99.9 %-
all-30578 --
Refinement stepCycle: LAST / Resolution: 1.58→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1813 0 0 189 2002
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.01
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.78

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