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- PDB-2fzu: Reduced enolate chromophore intermediate for GFP variant -

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Basic information

Entry
Database: PDB / ID: 2fzu
TitleReduced enolate chromophore intermediate for GFP variant
ComponentsGreen fluorescent protein
KeywordsLUMINESCENT PROTEIN / chromophore / intermediate / biosynthesis / post-translational modification / high resolution
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy / protein-chromophore linkage
Green fluorescent protein, GFP / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Green Fluorescent Protein / Beta Barrel / Mainly Beta
Green fluorescent protein
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsBarondeau, D.P. / Tainer, J.A. / Getzoff, E.D.
CitationJournal: J.Am.Chem.Soc. / Year: 2006
Title: Structural evidence for an enolate intermediate in GFP fluorophore biosynthesis.
Authors: Barondeau, D.P. / Tainer, J.A. / Getzoff, E.D.
Validation Report
SummaryFull reportAbout validation report
History
DepositionFeb 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 999SEQUENCE Ser 65 in the database has been mutated to THR. The residues THR 65, TYR 66 and GLY 67 ...SEQUENCE Ser 65 in the database has been mutated to THR. The residues THR 65, TYR 66 and GLY 67 constitute the chromophore C12 66.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9073
Polymers26,8201
Non-polymers862
Water6,413356
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)51.350, 62.520, 71.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe monomer in the assymetric unit is the biological assembly

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Components

#1: Protein Green fluorescent protein /


Mass: 26820.145 Da / Num. of mol.: 1 / Mutation: F64L, S65T, F99S, M153T, V163A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P42212
#2: Chemical ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.14 Å3/Da / Density % sol: 42.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50 mM MgCl2, 50 mM Hepes, 20% PEG 4K, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 28, 2000
RadiationMonochromator: Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.25→20 Å / Num. all: 154670 / Num. obs: 62613 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 9.9 Å2 / Rsym value: 0.045 / Net I/σ(I): 19.6
Reflection shellResolution: 1.25→1.29 Å / Mean I/σ(I) obs: 2.3 / Rsym value: 0.349 / % possible all: 91.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ema
Resolution: 1.25→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.199 3116 Random
Rwork0.142 --
All0.142 62451 -
Obs-59335 -
Refinement stepCycle: LAST / Resolution: 1.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1919 0 11 350 2280
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.022
X-RAY DIFFRACTIONs_angle_d0.032

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