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Yorodumi- PDB-3p9x: Crystal structure of phosphoribosylglycinamide formyltransferase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3p9x | ||||||
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Title | Crystal structure of phosphoribosylglycinamide formyltransferase from Bacillus Halodurans | ||||||
Components | phosphoribosylglycinamide formyltransferase | ||||||
Keywords | TRANSFERASE / Phosphoribosylglycinamide formyltransferase / PURINE BIOSYNTHESIS / Structural Genomics / PSI-biology / Protein Structure Initiative / New York Structural Genomics Research Consortium / NYSGRC | ||||||
Function / homology | Function and homology information phosphoribosylglycinamide formyltransferase 1 / phosphoribosylglycinamide formyltransferase activity / 'de novo' IMP biosynthetic process Similarity search - Function | ||||||
Biological species | Bacillus halodurans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Patskovsky, Y. / Toro, R. / Foti, R. / Seidel, R.D. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of phosphoribosylglycinamide formyltransferase from Bacillus Halodurans Authors: Patskovsky, Y. / Toro, R. / Foti, R. / Seidel, R.D. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3p9x.cif.gz | 99 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p9x.ent.gz | 75 KB | Display | PDB format |
PDBx/mmJSON format | 3p9x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3p9x_validation.pdf.gz | 458.3 KB | Display | wwPDB validaton report |
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Full document | 3p9x_full_validation.pdf.gz | 459.7 KB | Display | |
Data in XML | 3p9x_validation.xml.gz | 19.8 KB | Display | |
Data in CIF | 3p9x_validation.cif.gz | 28.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/3p9x ftp://data.pdbj.org/pub/pdb/validation_reports/p9/3p9x | HTTPS FTP |
-Related structure data
Related structure data | 2ywrS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23450.957 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus halodurans (bacteria) / Strain: C-125 / Gene: PURN / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KF54 #2: Chemical | ChemComp-SO4 / #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: 3.26 Å3/Da / Density % sol: 62.31 % |
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Crystal grow | pH: 6.5 Details: 0.1M SODIUM ACETATE, PH 4.5, 2M AMMONIUM SULFATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 24, 2010 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. obs: 48965 / % possible obs: 100 % / Observed criterion σ(I): -5 / Redundancy: 11.8 % / Biso Wilson estimate: 30.58 Å2 / Rsym value: 0.079 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 1.5 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: molecular replacement Starting model: PDB ENTRY 2YWR Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.645 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R Free: 0.117 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.89 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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