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Yorodumi- PDB-8su7: Crystal structure of Bacillus anthracis dihydroneopterin aldolase -
+Open data
-Basic information
Entry | Database: PDB / ID: 8su7 | ||||||
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Title | Crystal structure of Bacillus anthracis dihydroneopterin aldolase | ||||||
Components | 7,8-dihydroneopterin aldolase | ||||||
Keywords | LYASE / dihydroneopterin aldolase / DHNA | ||||||
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 (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Shaw, G.X. / Li, Y. / Yan, H. / Ji, X. | ||||||
Funding support | United States, 1items
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Citation | Journal: To be published Title: Crystal structure of Bacillus anthracis dihydroneopterin aldolase Authors: Shaw, G.X. / Li, Y. / Yan, H. / Ji, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8su7.cif.gz | 62.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8su7.ent.gz | 45.3 KB | Display | PDB format |
PDBx/mmJSON format | 8su7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8su7_validation.pdf.gz | 445.7 KB | Display | wwPDB validaton report |
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Full document | 8su7_full_validation.pdf.gz | 449.9 KB | Display | |
Data in XML | 8su7_validation.xml.gz | 12 KB | Display | |
Data in CIF | 8su7_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/su/8su7 ftp://data.pdbj.org/pub/pdb/validation_reports/su/8su7 | HTTPS FTP |
-Related structure data
Related structure data | 5f3mS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13994.912 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: folB, GBAA_0072 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6L7HSV1, dihydroneopterin aldolase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.44 Å3/Da / Density % sol: 49.69 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: CHO2Na, PEG3350, Ethylene glycol, etc. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 27, 2006 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→30 Å / Num. obs: 9468 / % possible obs: 90.2 % / Redundancy: 4.8 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.02 / Rrim(I) all: 0.045 / Χ2: 0.966 / Net I/σ(I): 17.2 / Num. measured all: 45448 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5F3M Resolution: 2.4→28.8 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 36.07 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→28.8 Å
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Refine LS restraints |
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LS refinement shell |
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