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Yorodumi- PDB-5f3m: Crystal structure of dihydroneopterin aldolase from Bacillus anth... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5f3m | ||||||
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Title | Crystal structure of dihydroneopterin aldolase from Bacillus anthracis complexed with L-neopterin at 1.5 Angstroms resolution . | ||||||
Components | 7,8-dihydroneopterin aldolase | ||||||
Keywords | ISOMERASE / aldolase / L-neopterin / alpha beta protein fold / Structural Genomics / PSI-Biology / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information dihydroneopterin aldolase / dihydroneopterin aldolase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus anthracis str. 'Ames Ancestor' (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.498 Å | ||||||
Authors | Maltseva, N. / Kim, Y. / Shatsman, S. / Anderson, W.F. / Joachimiak, A. / CSGID / Center for Structural Genomics of Infectious Diseases / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To Be Published Title: Crystal structure of dihydroneopterin aldolase from Bacillus anthracis complexed with L-neopterin at 1.5 Angstroms resolution . Authors: Maltseva, N. / Kim, Y. / Shatsman, S. / Anderson, W.F. / Joachimiak, A. / CSGID / Center for Structural Genomics of Infectious Diseases | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f3m.cif.gz | 134.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f3m.ent.gz | 104.3 KB | Display | PDB format |
PDBx/mmJSON format | 5f3m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5f3m_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5f3m_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5f3m_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 5f3m_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/5f3m ftp://data.pdbj.org/pub/pdb/validation_reports/f3/5f3m | HTTPS FTP |
-Related structure data
Related structure data | 1sqlS 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 on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 14360.960 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis str. 'Ames Ancestor' (bacteria) Gene: folB / Plasmid: pMCSG28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21magic References: UniProt: Q81VW7, UniProt: A0A6L7HSV1*PLUS, dihydroneopterin aldolase |
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-Non-polymers , 6 types, 248 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-FMT / | #7: 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: 3.54 Å3/Da / Density % sol: 65.3 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.02M magnesium chloride, 0.02M Nickel chloride, 0.1M Hepes pH 7.0, 20% PEG 3350 PH range: 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 19, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 66418 / % possible obs: 99.9 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 31.39 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 5 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.96 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SQL Resolution: 1.498→33.657 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 13.31 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.498→33.657 Å
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Refine LS restraints |
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LS refinement shell |
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