+Open data
-Basic information
Entry | Database: PDB / ID: 1yhg | ||||||
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Title | Uncyclized precursor structure of S65G Y66S V68G GFP variant | ||||||
Components | green fluorescent protein | ||||||
Keywords | LUMINESCENT PROTEIN / chromophore uncyclized dimer | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Barondeau, D.P. / Kassmann, C.J. / Tainer, J.A. / Getzoff, E.D. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Understanding GFP Chromophore Biosynthesis: Controlling Backbone Cyclization and Modifying Post-translational Chemistry. Authors: Barondeau, D.P. / Kassmann, C.J. / Tainer, J.A. / Getzoff, E.D. #1: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yhg.cif.gz | 100.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yhg.ent.gz | 76.6 KB | Display | PDB format |
PDBx/mmJSON format | 1yhg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yhg_validation.pdf.gz | 432 KB | Display | wwPDB validaton report |
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Full document | 1yhg_full_validation.pdf.gz | 433.4 KB | Display | |
Data in XML | 1yhg_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 1yhg_validation.cif.gz | 25.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yh/1yhg ftp://data.pdbj.org/pub/pdb/validation_reports/yh/1yhg | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 26692.943 Da / Num. of mol.: 2 / Mutation: F64L, S65G, Y66S, V68G, F99S, M153T, V163A Source method: isolated from a genetically manipulated source Details: F64L, S65G, Y66S, V68G, F99S, M153T, V163A / Source: (gene. exp.) Aequorea victoria (jellyfish) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P42212 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.8 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 4000, 50 mM MgCl2, 50 mM Hepes 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97975 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97975 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→100 Å / Num. obs: 13380 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.119 / Χ2: 1.528 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.312 / Num. unique all: 1324 / Χ2: 1.342 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→20 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 10 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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