+Open data
-Basic information
Entry | Database: PDB / ID: 2awj | ||||||
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Title | GFP R96M pre-cyclized intermediate in chromophore formation | ||||||
Components | green-fluorescent protein | ||||||
Keywords | LUMINESCENT PROTEIN / pre-cyclized chromophore-forming residues / GFP / barrel | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Wood, T.I. / Barondeau, D.P. / Hitomi, C. / Kassmann, C.J. / Tainer, J.A. / Getzoff, E.D. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Defining the role of arginine 96 in green fluorescent protein fluorophore biosynthesis. Authors: Wood, T.I. / Barondeau, D.P. / Hitomi, C. / 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 | 2awj.cif.gz | 67.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2awj.ent.gz | 46.9 KB | Display | PDB format |
PDBx/mmJSON format | 2awj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aw/2awj ftp://data.pdbj.org/pub/pdb/validation_reports/aw/2awj | HTTPS FTP |
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-Related structure data
Related structure data | 2awkC 2awlC 2awmC 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: 25751.959 Da / Num. of mol.: 1 / Fragment: residues 1-229 / Mutation: F64L, S65T, R96M, F99S, M153T, V163A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21/DE3 pRIL / References: UniProt: P42212 |
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#2: Chemical | ChemComp-MG / |
#3: 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: 2.24 Å3/Da / Density % sol: 45.09 % |
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Crystal grow | Temperature: 295 K / pH: 8 Details: PEG4000, magnesium chloride, Hepes, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 8.00 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 27, 2002 |
Radiation | Monochromator: 58 CM LONG, PT-COATED, FUSED SILICA, VERTICAL FOCUSMIRROR; CYCLINDRICALLY BENT TRIANGULAR SI(111) ASYMMETRIC CUT, HORIZONTAL FOCUS MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20 Å / Num. obs: 30130 / % possible obs: 96.9 % / Observed criterion σ(I): 5.4 / Redundancy: 3.8 % / Biso Wilson estimate: 17.3 Å2 / Rsym value: 0.086 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 5.4 / Rsym value: 0.426 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EMA Resolution: 1.6→20 Å / Num. parameters: 8373 / Num. restraintsaints: 7501 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 20.9 Å2
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 1751 / Occupancy sum non hydrogen: 2072
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Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.022
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