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- PDB-2g5z: Structure of S65G Y66S GFP variant after spontaneous peptide hydr... -

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Entry
Database: PDB / ID: 2g5z
TitleStructure of S65G Y66S GFP variant after spontaneous peptide hydrolysis and decarboxylation
Components(Green fluorescent protein) x 2
KeywordsLUMINESCENT PROTEIN / chromophore / biosynthesis / peptide hydrolysis / post-translational modification / decarboxylation
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 / 1.8 Å resolution
AuthorsBarondeau, D.P. / Kassmann, C.J. / Tainer, J.A. / Getzoff, E.D.
CitationJournal: J.Am.Chem.Soc. / Year: 2006
Title: Understanding GFP Posttranslational Chemistry: Structures of Designed Variants that Achieve Backbone Fragmentation, Hydrolysis, and Decarboxylation.
Authors: Barondeau, D.P. / Kassmann, C.J. / Tainer, J.A. / Getzoff, E.D.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 23, 2006 / Release: Apr 18, 2006
RevisionDateData content typeGroupProviderType
1.0Apr 18, 2006Structure modelrepositoryInitial release
1.1May 1, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
Remark 999SEQUENCE Ser 65 is mutated to Gly, Tyr 66 is mutated to Ser. Peptide bond at position 65-66 is ...SEQUENCE Ser 65 is mutated to Gly, Tyr 66 is mutated to Ser. Peptide bond at position 65-66 is broken and the C-terminus of residue 65 is decarboxylated forming NME. Residue S66 underwent side chain dehydration to create dehydroalanine moiety.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein
B: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7493
Polyers26,7252
Non-polymers241
Water5,765320
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)4630
ΔGint (kcal/M)-37
Surface area (Å2)10350
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)51.07, 62.57, 71.65
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP 21 21 21

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Components

#1: Protein/peptide Green fluorescent protein /


Mass: 6918.935 Da / Num. of mol.: 1 / Mutation: S65G / 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: Protein/peptide Green fluorescent protein /


Mass: 19806.074 Da / Num. of mol.: 1 / Mutation: Y66S, 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 42.55 %
Crystal growTemp: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50 mM MgCl2, 50 mM Hepes, 20% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.0

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: SSRL BEAMLINE BL9-1 / Synchrotron site: SSRL / Beamline: BL9-1 / Wavelength: 0.97946
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Collection date: Jul 4, 2004
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 13.1 Å2 / D resolution high: 1.8 Å / D resolution low: 2 Å / Number all: 21833 / Number obs: 21833 / Observed criterion sigma I: -3 / Rsym value: 0.086 / NetI over sigmaI: 28.8 / Percent possible obs: 1
Reflection shellHighest resolution: 1.8 Å / Lowest resolution: 1.86 Å / MeanI over sigI obs: 6.4 / Number unique all: 2135 / Rsym value: 0.343 / Percent possible all: 99.9

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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 / Cross valid method: THROUGHOUT / Sigma F: 0 / Stereochemistry target values: Engh & Huber
Least-squares processR factor R free: 0.232 / R factor R work: 0.16 / R factor all: 0.16 / Highest resolution: 1.8 Å / Lowest resolution: 2 Å / Number reflection R free: 1089 / Number reflection all: 21790 / Number reflection obs: 20701
Refine hist #LASTHighest resolution: 1.8 Å / Lowest resolution: 2 Å
Number of atoms included #LASTProtein: 1801 / Nucleic acid: 0 / Ligand: 7 / Solvent: 314 / Total: 2122
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.024

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