+Open data
-Basic information
Entry | Database: PDB / ID: 4ay3 | ||||||
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Title | Crystal structure of Bacillus anthracis PurE | ||||||
Components | N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE | ||||||
Keywords | LYASE / ISOMERASE | ||||||
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: 1.76 Å | ||||||
Authors | Oliete, R. / Pous, J. / Rodriguez-Puente, S. / Abad-Zapatero, C. / Guasch, A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Elastic and Inelastic Diffraction Changes Upon Variation of the Relative Humidity Environment of Pure Crystals Authors: Oliete, R. / Pous, J. / Rodriguez-Puente, S. / Abad-Zapatero, C. / Guasch, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ay3.cif.gz | 254 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ay3.ent.gz | 207 KB | Display | PDB format |
PDBx/mmJSON format | 4ay3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/4ay3 ftp://data.pdbj.org/pub/pdb/validation_reports/ay/4ay3 | HTTPS FTP |
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-Related structure data
Related structure data | 4ay4C 4b4kC 1xmpS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 19232.014 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS ANTHRACIS (anthrax bacterium) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q81ZH8, UniProt: A0A6L7HA71*PLUS, phosphoribosylaminoimidazole carboxylase, 5-(carboxyamino)imidazole ribonucleotide mutase #2: Chemical | ChemComp-ACT / #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: 2.06 Å3/Da / Density % sol: 40.15 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 0.75M SODIUM ACETATE, 0.1M CACODYLATE PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 |
Detector | Type: QUANTUM / Detector: CCD / Date: Mar 17, 2009 / Details: MULTILAYER |
Radiation | Monochromator: DIAMOND (111), GE(220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→50 Å / Num. obs: 57503 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.9 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 56.69 |
Reflection shell | Resolution: 1.76→1.82 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 8.07 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XMP Resolution: 1.76→49.53 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.81 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.099 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.719 Å2
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Refinement step | Cycle: LAST / Resolution: 1.76→49.53 Å
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Refine LS restraints |
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