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Yorodumi- PDB-1xmp: Crystal Structure of PurE (BA0288) from Bacillus anthracis at 1.8... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xmp | ||||||
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Title | Crystal Structure of PurE (BA0288) from Bacillus anthracis at 1.8 Resolution | ||||||
Components | phosphoribosylaminoimidazole carboxylase | ||||||
Keywords | LYASE / PurE / purine biosynthesis / BA0288 / Bacillus anthracis / SPINE | ||||||
Function / homology | Function and homology information 5-(carboxyamino)imidazole ribonucleotide mutase / 5-(carboxyamino)imidazole ribonucleotide mutase activity / 'de novo' IMP biosynthetic process / lyase activity Similarity search - Function | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Boyle, M.P. / Kalliomaa, A.K. / Levdikov, V. / Blagova, E. / Fogg, M.J. / Brannigan, J.A. / Wilkinson, A.J. / Wilson, K.S. | ||||||
Citation | Journal: Proteins / Year: 2005 Title: Crystal structure of PurE (BA0288) from Bacillus anthracis at 1.8 A resolution Authors: Boyle, M.P. / Kalliomaa, A.K. / Levdikov, V. / Blagova, E. / Fogg, M.J. / Brannigan, J.A. / Wilson, K.S. / Wilkinson, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xmp.cif.gz | 260.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xmp.ent.gz | 210 KB | Display | PDB format |
PDBx/mmJSON format | 1xmp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xm/1xmp ftp://data.pdbj.org/pub/pdb/validation_reports/xm/1xmp | HTTPS FTP |
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-Related structure data
Related structure data | 1qczS 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
#1: Protein | Mass: 18120.736 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: purE / Plasmid: pET-YSBLIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: Q81ZH8, UniProt: A0A6L7HA71*PLUS, phosphoribosylaminoimidazole carboxylase #2: 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: 2.4 Å3/Da / Density % sol: 48.5 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG 4000, sodium formate, TRIS, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 30, 2004 / Details: Rh coated Si mirror |
Radiation | Monochromator: Si monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 120128 / Num. obs: 120128 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 2.5 / Num. unique all: 11473 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QCZ Resolution: 1.8→31.14 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.563 / SU ML: 0.08 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.119 / ESU R Free: 0.115 / 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: 16.47 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→31.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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