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Yorodumi- PDB-3dcj: Crystal structure of glycinamide formyltransferase (PurN) from My... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dcj | ||||||
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Title | Crystal structure of glycinamide formyltransferase (PurN) from Mycobacterium tuberculosis in complex with 5-methyl-5,6,7,8-tetrahydrofolic acid derivative | ||||||
Components | Probable 5'-phosphoribosylglycinamide formyltransferase purN | ||||||
Keywords | TRANSFERASE / GLYCINAMIDE FORMYLTRANSFERASE / PurN | ||||||
Function / homology | Function and homology information phosphoribosylglycinamide formyltransferase 1 / phosphoribosylglycinamide formyltransferase activity / tetrahydrofolate metabolic process / 'de novo' IMP biosynthetic process / magnesium ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Zhang, Z. / Squire, C.J. / Baker, E.N. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Structures of glycinamide ribonucleotide transformylase (PurN) from Mycobacterium tuberculosis reveal a novel dimer with relevance to drug discovery. Authors: Zhang, Z. / Caradoc-Davies, T.T. / Dickson, J.M. / Baker, E.N. / Squire, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dcj.cif.gz | 96.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dcj.ent.gz | 72.5 KB | Display | PDB format |
PDBx/mmJSON format | 3dcj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/3dcj ftp://data.pdbj.org/pub/pdb/validation_reports/dc/3dcj | HTTPS FTP |
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-Related structure data
Related structure data | 3da8C 1meoS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 22409.627 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: purN, MT0983, Rv0956 / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P71554, UniProt: P9WHM5*PLUS, phosphoribosylglycinamide formyltransferase 1 |
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-Non-polymers , 5 types, 292 molecules
#2: Chemical | #3: Chemical | ChemComp-MG / | #4: Chemical | #5: Chemical | ChemComp-NO3 / | #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: 2.56 Å3/Da / Density % sol: 51.95 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% PEG 3350, 0.2 M Mg nitrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54178 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 2, 2007 |
Radiation | Monochromator: Osmic mirror focusing optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→32.58 Å / Num. all: 22471 / Num. obs: 22471 / % possible obs: 100 % / Biso Wilson estimate: 21.59 Å2 |
Reflection shell | Resolution: 2.2→2.34 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1MEO Resolution: 2.2→32.58 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.911 / SU B: 5.596 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.272 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES HAVE BEEN REFINED INDIVIDUALLY.
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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: 19.894 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→32.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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