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Yorodumi- PDB-4i4c: Crystal structure of the protein frsA complexed with unknown ligand -
+Open data
-Basic information
Entry | Database: PDB / ID: 4i4c | ||||||
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Title | Crystal structure of the protein frsA complexed with unknown ligand | ||||||
Components | UPF0255 protein frsA | ||||||
Keywords | UNKNOWN FUNCTION / two-domain protein frsA / unknown ligand | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Vibrio vulnificus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Fedorov, A.A. / Fedorov, E.V. / Desai, B. / Gerlt, J.A. / Richards, N. / Almo, S.C. | ||||||
Citation | Journal: Biochemistry / Year: 2013 Title: Computational, structural, and kinetic evidence that Vibrio vulnificus FrsA is not a cofactor-independent pyruvate decarboxylase. Authors: Kellett, W.F. / Brunk, E. / Desai, B.J. / Fedorov, A.A. / Almo, S.C. / Gerlt, J.A. / Rothlisberger, U. / Richards, N.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4i4c.cif.gz | 329.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4i4c.ent.gz | 269.5 KB | Display | PDB format |
PDBx/mmJSON format | 4i4c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4i4c_validation.pdf.gz | 815.4 KB | Display | wwPDB validaton report |
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Full document | 4i4c_full_validation.pdf.gz | 821.9 KB | Display | |
Data in XML | 4i4c_validation.xml.gz | 32.2 KB | Display | |
Data in CIF | 4i4c_validation.cif.gz | 45.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i4/4i4c ftp://data.pdbj.org/pub/pdb/validation_reports/i4/4i4c | HTTPS FTP |
-Related structure data
Related structure data | 3mveS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 47073.855 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio vulnificus (bacteria) / Gene: frsA / Production host: Escherichia coli (E. coli) / References: UniProt: D9IR22 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 20% PEG monomethyl ether 2000, 0.1M Tris, 0.2M Trimethylamine N-oxide, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 25, 2012 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→38.284 Å / Num. all: 51363 / Num. obs: 51363 / % possible obs: 97.79 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MVE Resolution: 1.95→38.284 Å / SU ML: 0.24 / σ(F): 0 / Phase error: 25.33 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→38.284 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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