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Yorodumi- PDB-1w7u: Photoproduct of the Wild-Type Aequorea victoria Green Fluorescent... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1w7u | |||||||||
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Title | Photoproduct of the Wild-Type Aequorea victoria Green Fluorescent Protein after structural annealing at 170K | |||||||||
Components | GREEN FLUORESCENT PROTEIN | |||||||||
Keywords | LUMINESCENT PROTEIN / BETA-BARREL / BIOLUMINESCENCE / PHOTOPRODUCT | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | AEQUOREA VICTORIA (jellyfish) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | |||||||||
Authors | Van Thor, J.J. / Georgiev, G.Y. / Towrie, M. / Sage, J.T. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Ultrafast and Low Barrier Motions in the Photoreactions of the Green Fluorescent Protein Authors: Van Thor, J.J. / Georgiev, G.Y. / Towrie, M. / Sage, J.T. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "BA" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "BA" IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY 12-STRANDED BARRELS REPRESENTED BY A 13-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" AND "DA" IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY 10-STRANDED BARRELS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w7u.cif.gz | 210 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w7u.ent.gz | 169.4 KB | Display | PDB format |
PDBx/mmJSON format | 1w7u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Data in XML | 1w7u_validation.xml.gz | 43.4 KB | Display | |
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Data in CIF | 1w7u_validation.cif.gz | 819 B | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/1w7u ftp://data.pdbj.org/pub/pdb/validation_reports/w7/1w7u | HTTPS FTP |
-Related structure data
Related structure data | 1w7sC 1w7tC 1hcjS 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: 26887.346 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Details: THE CHROMOPHORE (GYS, 5-(1-AMINO-2-HYDROXYETHYL)-1-CARBOXYMETHYL-3-((P-HYDROXYPHENYL)-METHYLENE)-IMIDAZOL-2-ONE)IS PART OF THE PEPTIDE CHAIN BETWEEN RESIDUES 64 AND 68. Source: (gene. exp.) AEQUOREA VICTORIA (jellyfish) / Tissue: CIRCUMORAL RING CANAL / Organ: PHOTOGENIC ORGAN / Production host: ESCHERICHIA COLI M15 (bacteria) / References: UniProt: P42212 #2: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | MODRES: GLU 222 SIDECHAIN IS SPECIFICALLY DECARBOXYLATED AS A RESULT OF PHOTOTRANSFORMATION. OE1, ...MODRES: GLU 222 SIDECHAIN IS SPECIFICAL | |
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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: 2.2 Å3/Da / Density % sol: 43 % |
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Crystal grow | Temperature: 277 K / pH: 7.8 Details: CRYSTALS WERE GROWN AT 4C FROM 50 MM MGCL2, 14-17 % PEG3350 AND 50-100 MM TRIS/CL PH 7.8 - 8.6. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.97809 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 8, 2003 / Details: RH COATED SILICON MIRROR |
Radiation | Monochromator: SILICON (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97809 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→33.15 Å / Num. obs: 85637 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 2.8 / % possible all: 84 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HCJ Resolution: 1.85→119.52 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.84 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.45 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→119.52 Å
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