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Yorodumi- PDB-3ai4: Crystal structure of yeast enhanced green fluorescent protein - m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ai4 | ||||||
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Title | Crystal structure of yeast enhanced green fluorescent protein - mouse polymerase iota ubiquitin binding motif fusion protein | ||||||
Components | yeast enhanced green fluorescent protein,DNA polymerase iota | ||||||
Keywords | Fluorescent Protein / replication / UBM / Ubiquitin-binding motif / GFP / Fusion | ||||||
Function / homology | Function and homology information Translesion synthesis by POLI / Termination of translesion DNA synthesis / cellular response to UV-C / translesion synthesis / serine-type endopeptidase inhibitor activity / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / extracellular space ...Translesion synthesis by POLI / Termination of translesion DNA synthesis / cellular response to UV-C / translesion synthesis / serine-type endopeptidase inhibitor activity / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / extracellular space / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Aequorea victoria (jellyfish) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Suzuki, N. / Wakatsuki, S. / Kawasaki, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2010 Title: Crystallization of small proteins assisted by green fluorescent protein Authors: Suzuki, N. / Hiraki, M. / Yamada, Y. / Matsugaki, N. / Igarashi, N. / Kato, R. / Dikic, I. / Drew, D. / Iwata, S. / Wakatsuki, S. / Kawasaki, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ai4.cif.gz | 122.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ai4.ent.gz | 93.3 KB | Display | PDB format |
PDBx/mmJSON format | 3ai4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ai4_validation.pdf.gz | 439.8 KB | Display | wwPDB validaton report |
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Full document | 3ai4_full_validation.pdf.gz | 441.2 KB | Display | |
Data in XML | 3ai4_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 3ai4_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/3ai4 ftp://data.pdbj.org/pub/pdb/validation_reports/ai/3ai4 | HTTPS FTP |
-Related structure data
Related structure data | 3ai5C 1gflS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 32090.928 Da / Num. of mol.: 1 Fragment: recidues 1-230 for yeast enhanced green fluorescent protein,UBIQUITIN BINDING MOTIF FUSION PROTEIN for DNA polymerase iota Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Mus musculus (house mouse) Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6R3M4, UniProt: P42212*PLUS | ||
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#2: Chemical | ChemComp-SO4 / | ||
#3: Water | ChemComp-HOH / | ||
Compound details | YEAST ENHANCED GREEN FLUORESCENSequence details | THE SEQUENCE OF YEAST ENHANCED GREEN FLUORESCENT PROTEIN HAS BEEN DEPOSITED IN GENBANK WITH ...THE SEQUENCE OF YEAST ENHANCED GREEN FLUORESCEN | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES, 2.0M Ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 19, 2009 / Details: mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→100 Å / Num. obs: 39422 / % possible obs: 90.7 % / Redundancy: 8.7 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 29 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 6.3 / Num. unique all: 2136 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GFL Resolution: 1.6→29 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.932 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.53 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.599→1.641 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 5.3408 Å / Origin y: 28.5551 Å / Origin z: 23.8434 Å
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Refinement TLS group |
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