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- PDB-3qff: Crystal Structure of ADP complex of purK: N5-carboxyaminoimidazol... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3qff | ||||||
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Title | Crystal Structure of ADP complex of purK: N5-carboxyaminoimidazole ribonucleotide synthetase | ||||||
![]() | N5-carboxyaminoimidazole ribonucleotide synthetase | ||||||
![]() | LYASE / carboxylase / ATP binding / ADP binding | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fung, L.W. / Tuntland, M.L. / Santarsiero, B.D. / Johnson, M.E. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 165.6 KB | Display | ![]() |
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PDB format | ![]() | 128.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 30.7 KB | Display | |
Data in CIF | ![]() | 44.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3r5hC ![]() 3v4sC ![]() 4dlkC ![]() 3q2oS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() References: UniProt: C3PBM5, phosphoribosylaminoimidazole carboxylase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.91 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M MES, 5mM DTT, 9% glycerol, 10% PEG6000, Hampton Research Silver Bullet Bio additive C3/27 and 3mM ADP, pH 6.5, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 2, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Highest resolution: 1.96 Å / Num. obs: 55699 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 39.42 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 14.43 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3Q2O Resolution: 1.96→19.97 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.2551 / WRfactor Rwork: 0.1987 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.841 / SU B: 4.24 / SU ML: 0.121 / SU R Cruickshank DPI: 0.1901 / SU Rfree: 0.1744 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.174 / 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: 68.43 Å2 / Biso mean: 34.6697 Å2 / Biso min: 12.81 Å2
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Refinement step | Cycle: LAST / Resolution: 1.96→19.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.961→2.012 Å / Total num. of bins used: 20
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