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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 / homologyGreen fluorescent protein, GFP / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / protein-chromophore linkage / Green fluorescent protein
Function and homology information
Specimen sourceAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 1.25 Å resolution
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
DateDeposition: Feb 10, 2006 / Release: Mar 14, 2006
RevisionDateData content typeGroupProviderType
1.0Mar 14, 2006Structure modelrepositoryInitial release
1.1May 1, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion 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
Polyers26,8201
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-MP 21 21 21
DetailsThe monomer in the assymetric unit is the biological assembly

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Components

#1: Protein/peptide Green fluorescent protein /


Mass: 26820.145 Da / Num. of mol.: 1 / Mutation: F64L, S65T, F99S, M153T, V163A / Source: (gene. exp.) Aequorea victoria (jellyfish) / Genus: Aequorea / Gene: GFP / Plasmid name: pET11a / Genus (production host): Escherichia / 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


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Formula: C2H6O2 / Ethylene glycol
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / Formula: H2O / Water

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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 / Density percent sol: 42.62 %
Crystal growTemp: 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 kelvins
SourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Collection date: Apr 28, 2000
RadiationMonochromator: Crystal / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 9.9 Å2 / D resolution high: 1.25 Å / D resolution low: 2 Å / Number all: 154670 / Number obs: 62613 / Observed criterion sigma I: -3 / Rsym value: 0.045 / NetI over sigmaI: 19.6 / Percent possible obs: 96.9
Reflection shellHighest resolution: 1.25 Å / Lowest resolution: 1.29 Å / MeanI over sigI obs: 2.3 / Rsym value: 0.349 / Percent possible all: 91.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ema
R Free selection details: Random / Sigma F: 0 / Stereochemistry target values: Engh & Huber
Least-squares processR factor R free: 0.199 / R factor R work: 0.142 / R factor all: 0.142 / Highest resolution: 1.25 Å / Lowest resolution: 2 Å / Number reflection R free: 3116 / Number reflection all: 62451 / Number reflection obs: 59335
Refine hist #LASTHighest resolution: 1.25 Å / Lowest resolution: 2 Å
Number of atoms included #LASTProtein: 1919 / Nucleic acid: 0 / Ligand: 11 / Solvent: 350 / Total: 2280
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.022
X-RAY DIFFRACTIONs_angle_d0.032

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