+Open data
-Basic information
Entry | Database: PDB / ID: 3fpe | ||||||
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Title | Crystal Structure of MtNAS in complex with thermonicotianamine | ||||||
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 / SAD / Resolution: 1.7 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 | 3fpe.cif.gz | 124.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fpe.ent.gz | 101.8 KB | Display | PDB format |
PDBx/mmJSON format | 3fpe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fpe_validation.pdf.gz | 997.3 KB | Display | wwPDB validaton report |
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Full document | 3fpe_full_validation.pdf.gz | 1003.4 KB | Display | |
Data in XML | 3fpe_validation.xml.gz | 26.7 KB | Display | |
Data in CIF | 3fpe_validation.cif.gz | 39.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/3fpe ftp://data.pdbj.org/pub/pdb/validation_reports/fp/3fpe | HTTPS FTP |
-Related 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: 33850.719 Da / Num. of mol.: 2 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: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.67 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 22% PEG 3350, 400mM NaBr, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.7→44.677 Å / Num. all: 71146 / Num. obs: 71075 / % possible obs: 98.5 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 5.43 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.7→39.56 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.058 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.108 / 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: 56.73 Å2 / Biso mean: 16.848 Å2 / Biso min: 5.31 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→39.56 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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