+Open data
-Basic information
Entry | Database: PDB / ID: 3i19 | ||||||
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Title | 1.4 Angstrom Crystal Structure of Fluorescent Protein Cypet | ||||||
Components | Green fluorescent protein | ||||||
Keywords | FLUORESCENT PROTEIN / BETA BARREL / CHROMOPHORE / LUMINESCENCE / PHOTOPROTEIN | ||||||
Function / homology | Function and homology information serine-type endopeptidase inhibitor activity / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å | ||||||
Authors | Hu, X. | ||||||
Citation | Journal: To be Published Title: 1.4 Angstrom Crystal Structure of Fluorescent Protein Cypet Authors: Liu, R. / Ding, Y. / Hu, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3i19.cif.gz | 68.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i19.ent.gz | 48.7 KB | Display | PDB format |
PDBx/mmJSON format | 3i19.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3i19_validation.pdf.gz | 434.2 KB | Display | wwPDB validaton report |
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Full document | 3i19_full_validation.pdf.gz | 438.9 KB | Display | |
Data in XML | 3i19_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 3i19_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i1/3i19 ftp://data.pdbj.org/pub/pdb/validation_reports/i1/3i19 | HTTPS FTP |
-Related structure data
Related structure data | 1qyoS 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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Unit cell |
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Details | AUTHOR STATES THAT THE BIOLOGICAL UNIT IS UNKNOWN. |
-Components
#1: Protein | Mass: 27496.031 Da / Num. of mol.: 1 / Mutation: T9G, V11I, D19E, A87V, I167A, E172T, L194I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pT7His-CyPet / Production host: Escherichia coli (E. coli) / References: UniProt: P42212 |
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#2: Water | ChemComp-HOH / |
Sequence details | THE SEQUENCE WAS MUTATED FROM SER & TYR TO THR & TRP, RESPECTIVELY, TO FORM CHROMOPHORE. THESE FIVE ...THE SEQUENCE WAS MUTATED FROM SER & TYR TO THR & TRP, RESPECTIVE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% PEG 4000, 0.1M Tris-HCl pH 8.5, 0.2M Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.0082 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 16, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0082 Å / Relative weight: 1 |
Reflection | Resolution: 1.36→50 Å / Num. obs: 49295 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Rmerge(I) obs: 0.047 / Rsym value: 0.042 / Net I/σ(I): 41 / Num. measured all: 550430 |
Reflection shell | Resolution: 1.36→1.38 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 6.1 / Num. unique all: 2238 / Rsym value: 0.201 / % possible all: 91.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QYO Resolution: 1.36→29.14 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.726 / SU ML: 0.031 / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.056 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.314 Å2
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Refinement step | Cycle: LAST / Resolution: 1.36→29.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.36→1.396 Å / Total num. of bins used: 20
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