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Yorodumi- PDB-1emg: GREEN FLUORESCENT PROTEIN (65-67 REPLACED BY CRO, S65T SUBSTITUTI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1emg | ||||||
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Title | GREEN FLUORESCENT PROTEIN (65-67 REPLACED BY CRO, S65T SUBSTITUTION, Q80R) | ||||||
Components | PROTEIN (GREEN FLUORESCENT PROTEIN) | ||||||
Keywords | GREENFLUORESCENT PROTEIN / BIOLUMINESCENCE / PHOTOACTIVE PROTEIN / FLUORESCENT TAG / PH TITRATION | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Elsliger, M.A. / Wachter, R.M. / Kallio, K. / Hanson, G.T. / Remington, S.J. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Structural and spectral response of green fluorescent protein variants to changes in pH. Authors: Elsliger, M.A. / Wachter, R.M. / Hanson, G.T. / Kallio, K. / Remington, S.J. #1: Journal: To be Published Title: Spectral and Structural Response of Gfp Mutants to Variations in Ph and Ionic Strength Authors: Wachter, R.M. / Elsliger-A, M. / Kallio, K. / Hanson, G.T. / Remington, S.J. #2: Journal: Structure / Year: 1998 Title: Structural Basis of Spectral Shifts in the Yellow-Emission Variants of Green Fluorescent Protein Authors: Wachter, R.M. / Elsliger-A, M. / Kallio, K. / Hanson, G.T. / Remington, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1emg.cif.gz | 60.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1emg.ent.gz | 42.1 KB | Display | PDB format |
PDBx/mmJSON format | 1emg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1emg_validation.pdf.gz | 421.5 KB | Display | wwPDB validaton report |
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Full document | 1emg_full_validation.pdf.gz | 427.5 KB | Display | |
Data in XML | 1emg_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 1emg_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/em/1emg ftp://data.pdbj.org/pub/pdb/validation_reports/em/1emg | HTTPS FTP |
-Related structure data
Related structure data | 1c4fC 1emaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26945.383 Da / Num. of mol.: 1 Mutation: 65 - 67 REPLACED BY CRO, S65T SUBSTITUTION, Q80R SUBSTITUTION Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Strain: JM109(DE3) / Tissue: CIRCUMORAL RING CANAL / Description: THE N-TERMINAL HIS-TAG HAS BEEN REMOVED / Organ: PHOTOGENIC ORGAN / Cellular location (production host): CYTAPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P42212 |
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#2: Water | ChemComp-HOH / |
Sequence details | THE FLUOROPHORE (CRO) IS GENERATED BY AN AUTOCATALYTIC CYCLIZATION OF THE POLYPEPTIDE BACKBONE ...THE FLUOROPHOR |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 42.17 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 Details: CRYSTALLIZATION CONDITIONS: 22-26% PEG 4000, 50 MM HEPES PH 8.0, 50 MM MGCL2, 12 MG PROTEIN | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.9 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 16011 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.075 |
Reflection shell | Resolution: 2→2.05 Å / % possible all: 94 |
Reflection | *PLUS Num. measured all: 93073 |
Reflection shell | *PLUS % possible obs: 94 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EMA Resolution: 2→20 Å / Isotropic thermal model: TNT / Stereochemistry target values: TNT
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Solvent computation | Solvent model: BABINET SCALING / Bsol: 148.1 Å2 / ksol: 0.769 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5F / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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