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Yorodumi- PDB-3r5h: Crystal Structure of ADP-AIR complex of purK: N5-carboxyaminoimid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3r5h | ||||||
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Title | Crystal Structure of ADP-AIR complex of purK: N5-carboxyaminoimidazole ribonucleotide synthetase | ||||||
Components | Phosphoribosylaminoimidazole carboxylase, ATPase subunit | ||||||
Keywords | LYASE / carboxylase | ||||||
Function / homology | Function and homology information Rossmann fold - #20 / ATP-grasp fold, A domain / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Fung, L.W. / Tuntland, M.L. / Santarsiero, B.D. / Johnson, M.E. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Elucidation of the bicarbonate binding site and insights into the carboxylation mechanism of (N(5))-carboxyaminoimidazole ribonucleotide synthase (PurK) from Bacillus anthracis Authors: Tuntland, M.L. / Santarsiero, B.D. / Johnson, M.E. / Fung, L.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3r5h.cif.gz | 176.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3r5h.ent.gz | 135.9 KB | Display | PDB format |
PDBx/mmJSON format | 3r5h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r5/3r5h ftp://data.pdbj.org/pub/pdb/validation_reports/r5/3r5h | HTTPS FTP |
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-Related structure data
Related structure data | 3qffC 3v4sC 4dlkC 3q20S 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43209.355 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: A0248 / Gene: BAA_0344, purK / Plasmid: pDEST15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL References: UniProt: C3PBM5, phosphoribosylaminoimidazole carboxylase #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.31 Å3/Da / Density % sol: 46.85 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M MES, 5mM DTT, 11% glycerol, 10% PEG 6000, Hampton Research Addition Screen Condition 46, 10mM MgCl2; Crystal soaked for one minute with 10mM AIR, pH 6.5, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: Feb 16, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→20 Å / Num. all: 41312 / Num. obs: 41312 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 35.399 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 22.57 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3Q20 Resolution: 2.2→19.76 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.904 / WRfactor Rfree: 0.2533 / WRfactor Rwork: 0.1835 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8389 / SU B: 5.672 / SU ML: 0.146 / SU R Cruickshank DPI: 0.2865 / SU Rfree: 0.2283 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 67.37 Å2 / Biso mean: 29.1989 Å2 / Biso min: 9.44 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→19.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.256 Å / Total num. of bins used: 20
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