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Yorodumi- PDB-2aha: Crystal structure analysis of a rate-enhanced variant of redox-se... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2aha | |||||||||
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Title | Crystal structure analysis of a rate-enhanced variant of redox-sensitive green fluorescent protein in the reduced form, roGFP1-R8. | |||||||||
Components | Green fluorescent protein | |||||||||
Keywords | LUMINESCENT PROTEIN / beta barrel / chromophore / disulfide | |||||||||
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: 1.98 Å | |||||||||
Authors | Cannon, M.B. / Remington, S.J. | |||||||||
Citation | Journal: Protein Sci. / Year: 2006 Title: Re-engineering redox-sensitive green fluorescent protein for improved response rate. Authors: Cannon, M.B. / Remington, S.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2aha.cif.gz | 107.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2aha.ent.gz | 79.9 KB | Display | PDB format |
PDBx/mmJSON format | 2aha.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ah/2aha ftp://data.pdbj.org/pub/pdb/validation_reports/ah/2aha | HTTPS FTP |
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-Related structure data
Related structure data | 2ah8C 1emaS C: citing same article (ref.) 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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Details | The biological unit is a monomer. There are 2 biological units in the asymmetric unit. |
-Components
#1: Protein | Mass: 26902.295 Da / Num. of mol.: 2 / Fragment: GFP / Mutation: Q80R,C48S,S147C,Q204C,K41D,F223R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pRSET-b / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P42212 #2: Chemical | ChemComp-SO4 / #3: 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: 3.1 Å3/Da / Density % sol: 60.6 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: sodium phosphate/citrate, ammonium sulfate, DTT, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 23, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. all: 45664 / Num. obs: 45355 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 10.4 % / Rmerge(I) obs: 0.141 / Χ2: 8.694 |
Reflection shell | Resolution: 1.95→2.02 Å / % possible obs: 99.9 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 50.7 / Num. measured obs: 4462 / Χ2: 3.323 / % possible all: 99.9 |
-Phasing
Phasing MR | Rfactor: 0.537 / Cor.coef. Fo:Fc: 0.285
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EMA Resolution: 1.98→50 Å / σ(F): 0 / Stereochemistry target values: TNT
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Solvent computation | Bsol: 150 Å2 / ksol: 0.8 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.98→50 Å
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Refine LS restraints |
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LS refinement shell |
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