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Yorodumi- PDB-5nhn: Super-Folder Green Fluorescent Protein Artificiall dimer linked v... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nhn | ||||||
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Title | Super-Folder Green Fluorescent Protein Artificiall dimer linked via 148 position | ||||||
Components | (Green fluorescent ...) x 2 | ||||||
Keywords | FLUORESCENT PROTEIN / Fluorescence / Dimer / click-chemistry / artificial dimer | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | ||||||
Authors | Worthy, H.L. / Rizkallah, P.J. | ||||||
Citation | Journal: Commun Chem / Year: 2019 Title: Positive functional synergy of structurally integrated artificial protein dimers assembled by Click chemistry Authors: Worthy, H.L. / Auhim, H.S. / Jamieson, W.D. / Pope, J.R. / Wall, A. / Batchelor, R. / Johnson, R.L. / Watkins, D.W. / Rizkallah, P.J. / Castell, O.K. / Jones, D.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nhn.cif.gz | 200.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nhn.ent.gz | 160.4 KB | Display | PDB format |
PDBx/mmJSON format | 5nhn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nh/5nhn ftp://data.pdbj.org/pub/pdb/validation_reports/nh/5nhn | HTTPS FTP |
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-Related structure data
Related structure data | 5btoS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Refine code: 0
NCS ensembles :
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-Components
-Green fluorescent ... , 2 types, 2 molecules BA
#1: Protein | Mass: 25821.072 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: gfp / Production host: Escherichia coli (E. coli) / References: UniProt: A0A059PIQ0, UniProt: P42212*PLUS |
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#2: Protein | Mass: 25839.066 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: gfp / Production host: Escherichia coli (E. coli) / References: UniProt: A0A059PIQ0, UniProt: P42212*PLUS |
-Non-polymers , 4 types, 248 molecules
#3: Chemical | ChemComp-DB5 / [( |
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#4: Chemical | ChemComp-GOL / |
#5: Chemical | ChemComp-EDO / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.29 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop Details: Condition C6 of the PACT Premier screen: 0.1 M PCTP Buffer, pH 9.0, 25% PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→67.71 Å / Num. obs: 41916 / % possible obs: 100 % / Redundancy: 21.8 % / Biso Wilson estimate: 41.03 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.079 / Net I/σ(I): 22.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5BTO Resolution: 1.96→67.71 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 7.236 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.127 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.833 Å2
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Refinement step | Cycle: 1 / Resolution: 1.96→67.71 Å
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Refine LS restraints |
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