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Yorodumi- PDB-2pfm: Crystal Structure of Adenylosuccinate Lyase (PurB) from Bacillus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pfm | ||||||
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Title | Crystal Structure of Adenylosuccinate Lyase (PurB) from Bacillus anthracis | ||||||
Components | Adenylosuccinate lyase | ||||||
Keywords | LYASE / Adenylosuccinate lyase / PurB / purine biosynthesis / BA0290 / Bacillus anthracis | ||||||
Function / homology | Function and homology information adenylosuccinate lyase / N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity / (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido) succinate lyase (fumarate-forming) activity / 'de novo' AMP biosynthetic process / 'de novo' IMP biosynthetic process Similarity search - Function | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Levdikov, V.M. / Blagova, E.V. / Baumgart, M. / Moroz, O.V. / Wilkinson, A.J. / Wilson, K.S. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Adenylosuccinate Lyase (PurB) from Bacillus anthracis Authors: Levdikov, V.M. / Blagova, E.V. / Wilkinson, A.J. / Wilson, K.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pfm.cif.gz | 362.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pfm.ent.gz | 294.5 KB | Display | PDB format |
PDBx/mmJSON format | 2pfm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pf/2pfm ftp://data.pdbj.org/pub/pdb/validation_reports/pf/2pfm | HTTPS FTP |
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-Related structure data
Related structure data | 1c3cS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 51117.145 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: purB / Plasmid: pET-YSBLIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: Q81ZH6, UniProt: A0A6L8PR48*PLUS, adenylosuccinate lyase #2: Chemical | #3: 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: 2.94 Å3/Da / Density % sol: 58.21 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: Sodium malonate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0004 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 17, 2007 / Details: Toroidal mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0004 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 78074 / Num. obs: 78074 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.1 % / Biso Wilson estimate: 32.963 Å2 / Rmerge(I) obs: 0.125 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.753 / Num. unique all: 1741 / % possible all: 42.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1C3C Resolution: 2→43.19 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.953 / SU B: 8.026 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.376 / ESU R Free: 0.136 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.697 Å2
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Refinement step | Cycle: LAST / Resolution: 2→43.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.002→2.054 Å / Total num. of bins used: 20
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