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- PDB-2g5z: Structure of S65G Y66S GFP variant after spontaneous peptide hydr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2g5z | ||||||
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Title | Structure of S65G Y66S GFP variant after spontaneous peptide hydrolysis and decarboxylation | ||||||
![]() | (Green fluorescent protein) x 2 | ||||||
![]() | LUMINESCENT PROTEIN / chromophore / biosynthesis / peptide hydrolysis / post-translational modification / decarboxylation | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Barondeau, D.P. / Kassmann, C.J. / Tainer, J.A. / Getzoff, E.D. | ||||||
![]() | ![]() 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. | ||||||
History |
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Remark 999 | SEQUENCE 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 viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 68.4 KB | Display | ![]() |
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PDB format | ![]() | 47.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.5 KB | Display | ![]() |
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Full document | ![]() | 435.4 KB | Display | |
Data in XML | ![]() | 14.5 KB | Display | |
Data in CIF | ![]() | 21.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2g16C ![]() 2g2sC ![]() 2g3dC ![]() 2g6eC ![]() 1emaS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 6918.935 Da / Num. of mol.: 1 / Mutation: S65G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 19806.074 Da / Num. of mol.: 1 / Mutation: Y66S, F99S, M153T, V163A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.55 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 4, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 21833 / Num. obs: 21833 / % possible obs: 100 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 13.1 Å2 / Rsym value: 0.086 / Net I/σ(I): 28.8 |
Reflection shell | Resolution: 1.8→1.86 Å / Mean I/σ(I) obs: 6.4 / Num. unique all: 2135 / Rsym value: 0.343 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ema Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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