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Yorodumi- PDB-2hrs: Crystal structure of L42H V224H design intermediate for GFP metal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hrs | ||||||
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Title | Crystal structure of L42H V224H design intermediate for GFP metal ion reporter | ||||||
Components | Green fluorescent protein | ||||||
Keywords | LUMINESCENT PROTEIN / metal site design / intermediate / GFP / fluorophore / reporter | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Barondeau, D.P. / Tubbs, J.L. / Tainer, J.A. / Getzoff, E.D. | ||||||
Citation | Journal: To be Published Title: Iterative Structure-Based Design of a Green Fluorescent Protein Metal Ion Reporter Authors: Barondeau, D.P. / Tubbs, J.L. / Tainer, J.A. / Getzoff, E.D. | ||||||
History |
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Remark 999 | SEQUENCE AT POSITION 65, SER IS MUTATED TO THR, S65T. CHROMOPHORE CRO 66 RESULTS FROM THE ...SEQUENCE AT POSITION 65, SER IS MUTATED TO THR, S65T. CHROMOPHORE CRO 66 RESULTS FROM THE CYCLIZATION DEHYDRATION OF RESIDUES THR65-TYR66-GLY67. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hrs.cif.gz | 68.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hrs.ent.gz | 48.3 KB | Display | PDB format |
PDBx/mmJSON format | 2hrs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hr/2hrs ftp://data.pdbj.org/pub/pdb/validation_reports/hr/2hrs | HTTPS FTP |
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-Related structure data
Related structure data | 2hjoC 2hqzC 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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Unit cell |
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-Components
#1: Protein | Mass: 26828.066 Da / Num. of mol.: 1 / Mutation: F64L S65T F99S M153T V163A L42H V224H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: P42212 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-EDO / |
#4: 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: 2.12 Å3/Da / Density % sol: 41.95 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 19% PEG 4K, 50 mM MgCl2, 50 mM Hepes, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 2, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→20 Å / Num. obs: 43831 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 12.9 Å2 / Rsym value: 0.051 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 1.4→1.45 Å / Mean I/σ(I) obs: 3.6 / Num. unique all: 4146 / Rsym value: 0.337 / % possible all: 91.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1ema Resolution: 1.4→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.4→20 Å
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Refine LS restraints |
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