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Yorodumi- PDB-3wjc: Crystal structure of mutant nitrobindin M75L/H76L/Q96C/M148L/H158... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wjc | ||||||
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Title | Crystal structure of mutant nitrobindin M75L/H76L/Q96C/M148L/H158L covalently linked with [Rh(Cp-Mal)(COD)] (NB4-Rh) from Arabidopsis thaliana | ||||||
Components | UPF0678 fatty acid-binding protein-like protein At1g79260 | ||||||
Keywords | TRANSPORT PROTEIN / beta-barrel / intracellular transport / hydrophobic ligands / [Rh(Cp-Mal)(COD)] | ||||||
Function / homology | Function and homology information Isomerases; Other isomerases / isomerase activity / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Mizohata, E. / Fukumoto, K. / Onoda, A. / Bocola, M. / Arlt, M. / Inoue, T. / Schwaneberg, U. / Hayashi, T. | ||||||
Citation | Journal: CHEMCATCHEM / Year: 2014 Title: A Rhodium Complex-linked Hybrid Biocatalyst: Stereo-controlled Phenylacetylene Polymerization within an Engineered Protein Cavity Authors: Fukumoto, K. / Onoda, A. / Mizohata, E. / Bocola, M. / Inoue, T. / Schwaneberg, U. / Hayashi, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wjc.cif.gz | 130.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wjc.ent.gz | 108.6 KB | Display | PDB format |
PDBx/mmJSON format | 3wjc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wjc_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 3wjc_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 3wjc_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | 3wjc_validation.cif.gz | 28.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wj/3wjc ftp://data.pdbj.org/pub/pdb/validation_reports/wj/3wjc | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 19439.068 Da / Num. of mol.: 2 / Mutation: M75L, H76L, Q96C, M148L, H158L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g79260, At1g79260.1, YUP8H12R.14 / Plasmid: pET42b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star(DE3) / References: UniProt: O64527 #2: Chemical | #3: Chemical | ChemComp-BA / #4: 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: 3.85 Å3/Da / Density % sol: 68.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 5mM MES, 200mM NaCl, 100mM MES, 26% polyethylene glycol 400 , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å | |||||||||||||||
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Sep 14, 2013 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2→50 Å / Num. obs: 38003 / % possible obs: 95.9 % / Rsym value: 0.091 / Net I/σ(I): 11.1 | |||||||||||||||
Reflection shell | Resolution: 2→2.07 Å / Mean I/σ(I) obs: 3 / Rsym value: 0.357 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.874 / SU B: 8.237 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 40.307 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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