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Yorodumi- PDB-1hcj: Photoproduct of the wild-type Aequorea victoria Green Fluorescent... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hcj | |||||||||
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Title | Photoproduct of the wild-type Aequorea victoria Green Fluorescent Protein | |||||||||
Components | GREEN FLUORESCENT PROTEIN | |||||||||
Keywords | LUMINESCENT PROTEIN / FLUORESCENT PROTEIN / BETA-BARREL / BIOLUMINESCENCE / LUMINESCENCE | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | AEQUOREA VICTORIA (jellyfish) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Van Thor, J.J. / Gensch, T. / Hellingwerf, K.J. / Johnson, L. | |||||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2002 Title: Phototransformation of Green Fluorescent Protein with Uv and Visible Light Leads to Decarboxylation of Glutamate 222 Authors: Van Thor, J.J. / Gensch, T. / Hellingwerf, K.J. / Johnson, L. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEET PRESENTED FOR EACH CHAIN ON SHEET RECORDS BELOW IS ... SHEET DETERMINATION METHOD: DSSP THE SHEET PRESENTED FOR EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THAT IS REPRESENTED BY A 12-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 | 1hcj.cif.gz | 204.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hcj.ent.gz | 163.3 KB | Display | PDB format |
PDBx/mmJSON format | 1hcj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hcj_validation.pdf.gz | 462.9 KB | Display | wwPDB validaton report |
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Full document | 1hcj_full_validation.pdf.gz | 507.7 KB | Display | |
Data in XML | 1hcj_validation.xml.gz | 47.9 KB | Display | |
Data in CIF | 1hcj_validation.cif.gz | 64.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hc/1hcj ftp://data.pdbj.org/pub/pdb/validation_reports/hc/1hcj | HTTPS FTP |
-Related structure data
Related structure data | 1gflS S: Starting model for refinement |
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Similar 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: 26887.346 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) AEQUOREA VICTORIA (jellyfish) / Tissue: CIRCUMORAL RING CANAL / Gene: GFP / Organ: PHOTOGENIC ORGAN / Cellular location (production host): CYTOPLASM / Gene (production host): GFP / Production host: ESCHERICHIA COLI M15 (bacteria) / References: UniProt: P42212 #2: Water | ChemComp-HOH / | Compound details | MUTATION GLN80ARG OTHER_DETAILS: THE CHROMOPHORE, P-HYDROXYBENZYLIDENE-IMIDAZOLIDINONE (GYS), IS ...MUTATION GLN80ARG OTHER_DETAILS: THE CHROMOPHOR | Sequence details | MODRES: 1HCJ GYS A 66() GLU 222 SIDECHAIN IS SPECIFICALLY DECARBOXYLATED AS A RESULT OF ...MODRES: 1HCJ GYS A 66() 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: 2.34 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. | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 15, 2000 / Details: SAGITALLY FOCUSING GE(220 |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→33.15 Å / Num. obs: 92677 / % possible obs: 97.6 % / Observed criterion σ(I): 1.5 / Redundancy: 1.9 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 4 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 2.7 / % possible all: 96.8 |
Reflection | *PLUS Num. measured all: 519063 |
Reflection shell | *PLUS % possible obs: 96.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GFL Resolution: 1.8→33.15 Å / SU B: 3.82 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.151
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Displacement parameters | Biso mean: 32.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→33.15 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.209 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |