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Yorodumi- PDB-4nv1: Crystal structure of a 4-N formyltransferase from Francisella tul... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nv1 | ||||||
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Title | Crystal structure of a 4-N formyltransferase from Francisella tularensis | ||||||
Components | Formyltransferase | ||||||
Keywords | TRANSFERASE / FMT formyltransferase / N-10-formyl-tetrahydrofolate / formylation | ||||||
Function / homology | Function and homology information hydroxymethyl-, formyl- and related transferase activity / biosynthetic process Similarity search - Function | ||||||
Biological species | Francisella tularensis subsp. tularensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Thoden, J.B. / Zimmer, A.L. / Holden, H.M. | ||||||
Citation | Journal: Protein Sci. / Year: 2014 Title: Three-dimensional structure of a sugar N-formyltransferase from Francisella tularensis. Authors: Zimmer, A.L. / Thoden, J.B. / Holden, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nv1.cif.gz | 412.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nv1.ent.gz | 337.9 KB | Display | PDB format |
PDBx/mmJSON format | 4nv1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nv1_validation.pdf.gz | 3.2 MB | Display | wwPDB validaton report |
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Full document | 4nv1_full_validation.pdf.gz | 3.2 MB | Display | |
Data in XML | 4nv1_validation.xml.gz | 82.3 KB | Display | |
Data in CIF | 4nv1_validation.cif.gz | 110.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nv/4nv1 ftp://data.pdbj.org/pub/pdb/validation_reports/nv/4nv1 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Details | The symmetric unit deposited contains FOUR dimers |
-Components
-Protein , 1 types, 8 molecules CDEFBAGH
#1: Protein | Mass: 28063.061 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria) Strain: Schu S4 / Gene: wbtJ / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q79RC8, UniProt: Q5NF01*PLUS |
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-Non-polymers , 5 types, 745 molecules
#2: Chemical | ChemComp-0FX / #3: Chemical | ChemComp-PO4 / #4: Chemical | #5: Chemical | ChemComp-4TG / | #6: 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: 2.68 Å3/Da / Density % sol: 54.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 12-15% PEG8000, 100 mM HEPPS, 5 mM dTDP-Qui4NFo, 5 mM N5-THF, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 12, 2012 |
Radiation | Monochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 121975 / Num. obs: 121975 / % possible obs: 90.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 24 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 3.9 / Num. unique all: 11250 / Rsym value: 0.231 / % possible all: 82.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→29.96 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.9 / SU B: 6.161 / SU ML: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.247 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: S
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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 mean: 39.769 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→29.96 Å
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Refine LS restraints |
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