+Open data
-Basic information
Entry | Database: PDB / ID: 3o31 | ||||||
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Title | E81Q mutant of MtNAS in complex with a reaction intermediate | ||||||
Components | ThermoNicotianamine Synthase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Rossmann fold / thermonicotianamine synthase | ||||||
Function / homology | Function and homology information nicotianamine synthase activity / nicotianamine biosynthetic process / identical protein binding Similarity search - Function | ||||||
Biological species | Methanothermobacter thermautotrophicus str. Delta H (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å | ||||||
Authors | Dreyfus, C. / Pignol, D. / Arnoux, P. | ||||||
Citation | Journal: Chem.Commun.(Camb.) / Year: 2011 Title: The crystallographic structure of thermoNicotianamine synthase with a synthetic reaction intermediate highlights the sequential processing mechanism. Authors: Dreyfus, C. / Larrouy, M. / Cavelier, F. / Martinez, J. / Pignol, D. / Arnoux, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3o31.cif.gz | 141.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o31.ent.gz | 108.1 KB | Display | PDB format |
PDBx/mmJSON format | 3o31.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3o31_validation.pdf.gz | 463 KB | Display | wwPDB validaton report |
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Full document | 3o31_full_validation.pdf.gz | 470.4 KB | Display | |
Data in XML | 3o31_validation.xml.gz | 37.6 KB | Display | |
Data in CIF | 3o31_validation.cif.gz | 55.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o3/3o31 ftp://data.pdbj.org/pub/pdb/validation_reports/o3/3o31 | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 33603.453 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 2-265 / Mutation: E81Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus str. Delta H (archaea) Gene: MTH675, MTH_675 / Production host: Escherichia coli (E. coli) / References: UniProt: O26771 #2: Chemical | #3: Chemical | ChemComp-BR / #4: Water | ChemComp-HOH / | Has protein modification | Y | |
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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: 2.4 Å3/Da / Density % sol: 48.68 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 100 mM Bis-tris-propane, 20% (w/v) PEG3350, 200 mM NaBr, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97618 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 13, 2009 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97618 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→35 Å / Num. obs: 63699 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.7→1.79 Å / Rmerge(I) obs: 0.438 / % possible all: 97.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→32.39 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.109 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.114 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.36 Å2 / Biso mean: 16.5022 Å2 / Biso min: 2.33 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→32.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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