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Yorodumi- PDB-1kyp: Crystal Structure of an Apo Green Fluorescent Protein Zn Biosensor -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kyp | ||||||
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Title | Crystal Structure of an Apo Green Fluorescent Protein Zn Biosensor | ||||||
Components | Green Fluorescent Protein | ||||||
Keywords | LUMINESCENT PROTEIN / beta barrel / chromophore / apo structure | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Barondeau, D.P. / Kassmann, C.J. / Tainer, J.A. / Getzoff, E.D. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2002 Title: Structural chemistry of a green fluorescent protein Zn biosensor. Authors: Barondeau, D.P. / Kassmann, C.J. / Tainer, J.A. / Getzoff, E.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kyp.cif.gz | 123.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kyp.ent.gz | 93.3 KB | Display | PDB format |
PDBx/mmJSON format | 1kyp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kyp_validation.pdf.gz | 419.5 KB | Display | wwPDB validaton report |
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Full document | 1kyp_full_validation.pdf.gz | 421.3 KB | Display | |
Data in XML | 1kyp_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 1kyp_validation.cif.gz | 24 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ky/1kyp ftp://data.pdbj.org/pub/pdb/validation_reports/ky/1kyp | HTTPS FTP |
-Related structure data
Related structure data | 1kyrC 1kysC 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: 26712.008 Da / Num. of mol.: 1 / Mutation: F64L/S65T/Y66H/F99S/Y145F/H148G/M153T/V163A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: p42212, UniProt: P42212*PLUS |
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#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
Sequence details | RESIDUES 65SER AND 66TYR ARE MUTATED TO 65THR AND 66HIS. 65THR, 66HIS AND 67GLY ARE MODIFIED TO ...RESIDUES 65SER AND 66TYR ARE MUTATED TO 65THR AND 66HIS. 65THR, 66HIS AND 67GLY ARE MODIFIED TO MAKE THE CHROMOPHOR |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 42.33 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 4000, magnesium chloride, hepes, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: used microseeding | |||||||||||||||||||||||||||||||||||
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: SSRL / Beamline: BL9-2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 30, 2000 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→30 Å / Num. all: 162414 / Num. obs: 155872 / % possible obs: 97.5 % / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Biso Wilson estimate: 10.8 Å2 / Rsym value: 0.059 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 1.35→1.4 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.296 / % possible all: 88 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. obs: 49764 / Num. measured all: 162414 / Rmerge(I) obs: 0.059 |
Reflection shell | *PLUS % possible obs: 88 % / Rmerge(I) obs: 0.296 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ema Resolution: 1.35→20 Å / Num. parameters: 19933 / Num. restraintsaints: 23492 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-22 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 4 / Occupancy sum hydrogen: 1744 / Occupancy sum non hydrogen: 2201.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / Rfactor obs: 0.151 / Rfactor Rfree: 0.218 / Rfactor Rwork: 0.151 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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