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Yorodumi- PDB-3fph: Crystal Structure of E81Q mutant of MtNAS in complex with L-Glutamate -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fph | ||||||
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Title | Crystal Structure of E81Q mutant of MtNAS in complex with L-Glutamate | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | BIOSYNTHETIC PROTEIN / TRANSFERASE / thermonicotianamine / nicotianamine | ||||||
Function / homology | Function and homology information nicotianamine synthase activity / nicotianamine biosynthetic process / identical protein binding Similarity search - Function | ||||||
Biological species | Methanothermobacter thermautotrophicus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Dreyfus, C. / Pignol, D. / Arnoux, P. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Crystallographic snapshots of iterative substrate translocations during nicotianamine synthesis in Archaea Authors: Dreyfus, C. / Lemaire, D. / Mari, S. / 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 | 3fph.cif.gz | 135 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fph.ent.gz | 104.3 KB | Display | PDB format |
PDBx/mmJSON format | 3fph.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fph_validation.pdf.gz | 462.2 KB | Display | wwPDB validaton report |
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Full document | 3fph_full_validation.pdf.gz | 475.8 KB | Display | |
Data in XML | 3fph_validation.xml.gz | 30.9 KB | Display | |
Data in CIF | 3fph_validation.cif.gz | 46.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/3fph ftp://data.pdbj.org/pub/pdb/validation_reports/fp/3fph | HTTPS FTP |
-Related structure data
Related structure data | 3fpeSC 3fpfC 3fpgC 3fpjC 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: 33849.734 Da / Num. of mol.: 2 / Mutation: E81Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea) Gene: MTH675 / Plasmid: pET101 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O26771 #2: Chemical | #3: Chemical | #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: 2.5 Å3/Da / Density % sol: 50.79 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 22% PEG 3350, 400mM NaBr, pH 8, vapor diffusion, hanging drop, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9685 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 17, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9685 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→66.227 Å / Num. all: 63178 / Num. obs: 61535 / % possible obs: 97.4 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 5.415 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3FPE Resolution: 1.8→60.3 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.93 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.733 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.133 / 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: 81.65 Å2 / Biso mean: 28.107 Å2 / Biso min: 12.21 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→60.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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