+Open data
-Basic information
Entry | Database: PDB / ID: 2fwq | ||||||
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Title | Reduced enolate chromophore intermediate for Y66H GFP variant | ||||||
Components | Green fluorescent protein | ||||||
Keywords | LUMINESCENT PROTEIN / Beta barrel / chromophore / biosynthesis / intermediate / enolate / dithionite | ||||||
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: 1.4 Å | ||||||
Authors | Barondeau, D.P. / Tainer, J.A. / Getzoff, E.D. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2006 Title: Structural evidence for an enolate intermediate in GFP fluorophore biosynthesis. Authors: Barondeau, D.P. / Tainer, J.A. / Getzoff, E.D. | ||||||
History |
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Remark 999 | SEQUENCE Ser 65 in the database had been mutated to Thr, Tyr 66 to His. The residues Thr 65, His 66 ...SEQUENCE Ser 65 in the database had been mutated to Thr, Tyr 66 to His. The residues Thr 65, His 66 and Gly 67 constitute the chromophore XXY |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fwq.cif.gz | 70.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fwq.ent.gz | 48.8 KB | Display | PDB format |
PDBx/mmJSON format | 2fwq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2fwq_validation.pdf.gz | 427 KB | Display | wwPDB validaton report |
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Full document | 2fwq_full_validation.pdf.gz | 428.8 KB | Display | |
Data in XML | 2fwq_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 2fwq_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fw/2fwq ftp://data.pdbj.org/pub/pdb/validation_reports/fw/2fwq | HTTPS FTP |
-Related structure data
Related structure data | 2fzuC 1emaS S: Starting model for refinement C: citing same article (ref.) |
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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: 26729.016 Da / Num. of mol.: 1 / Mutation: F64L, S65T, Y66H, F99S, H148G, M153T, V163A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pET11 / 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: 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: 2.13 Å3/Da / Density % sol: 42.38 % |
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Crystal grow | Temperature: 298 K / pH: 8 Details: 50 mM MgCl2, 50 mM Hepes, 20% PEG 4000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 18, 2001 |
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: 44393 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 14.4 Å2 / Rsym value: 0.046 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 1.4→1.45 Å / Mean I/σ(I) obs: 3.1 / Rsym value: 0.353 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EMA Resolution: 1.4→20 Å / Num. restraintsaints: 19988 / σ(F): 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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