+Open data
-Basic information
Entry | Database: PDB / ID: 1q4d | ||||||
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Title | S65T Q80R T203C Green Fluorescent Protein (GFP) pH 5.5 | ||||||
Components | Green Fluorescent Protein | ||||||
Keywords | LUMINESCENT PROTEIN / green fluorescent protein / GFP / fluorophore / chromophore | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||
Authors | Jain, R.K. / Ranganathan, R. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2004 Title: Local complexity of amino acid interactions in a protein core. Authors: Jain, R.K. / Ranganathan, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q4d.cif.gz | 61.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q4d.ent.gz | 44.4 KB | Display | PDB format |
PDBx/mmJSON format | 1q4d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1q4d_validation.pdf.gz | 430.1 KB | Display | wwPDB validaton report |
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Full document | 1q4d_full_validation.pdf.gz | 432.5 KB | Display | |
Data in XML | 1q4d_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 1q4d_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q4/1q4d ftp://data.pdbj.org/pub/pdb/validation_reports/q4/1q4d | HTTPS FTP |
-Related structure data
Related structure data | 1q4aC 1q4bC 1q4cC 1q4eC 1q73C 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: 26947.422 Da / Num. of mol.: 1 / Mutation: Q80R, S65T, T203C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Plasmid: pRSET-B (Invitrogen) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P42212 |
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#2: Water | ChemComp-HOH / |
Sequence details | RESIDUE SER A 65 IS MUTATED TO THR A 65. THR A 65, TYR A 66 AND GLY A 67 ARE MODIFIED TO MAKE ...RESIDUE SER A 65 IS MUTATED TO THR A 65. THR A 65, TYR A 66 AND GLY A 67 ARE MODIFIED TO MAKE CHROMOPHOR |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.19 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG 4000, MgCl2, BME, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / PH range low: 8.5 / PH range high: 8.1 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.58→25 Å / Num. all: 30578 / Num. obs: 30578 / % possible obs: 99.9 % |
Reflection | *PLUS Redundancy: 4.7 % / Rmerge(I) obs: 0.046 |
Reflection shell | *PLUS % possible obs: 99.4 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EMA Resolution: 1.58→25 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.58→25 Å
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Refine LS restraints | *PLUS
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