[English] 日本語
Yorodumi- PDB-1qyf: Crystal structure of matured green fluorescent protein R96A variant -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qyf | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of matured green fluorescent protein R96A variant | ||||||
Components | green-fluorescent protein | ||||||
Keywords | LUMINESCENT PROTEIN / beta barrel / chromophore | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Barondeau, D.P. / Putnam, C.D. / Kassmann, C.J. / Tainer, J.A. / Getzoff, E.D. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2003 Title: Mechanism and energetics of green fluorescent protein chromophore synthesis revealed by trapped intermediate structures. Authors: Barondeau, D.P. / Putnam, C.D. / Kassmann, C.J. / Tainer, J.A. / Getzoff, E.D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1qyf.cif.gz | 117 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1qyf.ent.gz | 88.2 KB | Display | PDB format |
PDBx/mmJSON format | 1qyf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qy/1qyf ftp://data.pdbj.org/pub/pdb/validation_reports/qy/1qyf | HTTPS FTP |
---|
-Related structure data
Related structure data | 1qxtC 1qy3C 1qyoC 1qyqC 1emaS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 25671.809 Da / Num. of mol.: 1 / Fragment: residues 1-229 Mutation: R96A, F99S, M153T, V163A, F64L, S65CRO, Y66CRO, G67CRO Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P42212 |
---|---|
#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-EDO / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.68 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 4000, Magnesium Chloride, Hepes, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 27, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→40 Å / Num. all: 37602 / Num. obs: 34756 / % possible obs: 92.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.74 % / Biso Wilson estimate: 15.8 Å2 / Rsym value: 0.052 / Net I/σ(I): 27.4 |
Reflection shell | Resolution: 1.5→1.55 Å / Mean I/σ(I) obs: 3 / Rsym value: 0.253 / % possible all: 60.7 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ema Resolution: 1.5→40 Å / Num. parameters: 18771 / Num. restraintsaints: 22556 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.0196
| |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 1737 / Occupancy sum non hydrogen: 2084 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→40 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
|