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Open data
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Basic information
Entry | Database: PDB / ID: 3eth | ||||||
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Title | Crystal structure of E. coli Purk in complex with MgATP | ||||||
![]() | Phosphoribosylaminoimidazole carboxylase ATPase subunit | ||||||
![]() | LYASE / ATP-grasp / purine biosynthesis / antimicrobial / ATP-binding / Decarboxylase / Nucleotide-binding | ||||||
Function / homology | ![]() 5-(carboxyamino)imidazole ribonucleotide synthase / 5-(carboxyamino)imidazole ribonucleotide synthase activity / phosphoribosylaminoimidazole carboxylase activity / 'de novo' IMP biosynthetic process / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Holden, H.M. / Thoden, J.B. | ||||||
![]() | ![]() Title: Structural analysis of the active site geometry of N(5)-Carboxyaminoimidazole ribonucleotide synthetase from Escherichia coli. Authors: Thoden, J.B. / Holden, H.M. / Firestine, S.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 169.4 KB | Display | ![]() |
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PDB format | ![]() | 131.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 37.1 KB | Display | |
Data in CIF | ![]() | 54.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3etjC ![]() 1b6sS C: citing same article ( S: Starting model for refinement |
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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: 39528.000 Da / Num. of mol.: 2 / Mutation: E61Q, Q205R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P09029, phosphoribosylaminoimidazole carboxylase #2: Chemical | #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.9 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20-25% monomethylether poly(ethylene glycol) 5000, 10 mM MgATP, 10 mM aminopyrazole ribonucleotide, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: SBC-3 / Detector: CCD / Date: Dec 6, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30 Å / Num. all: 87837 / Num. obs: 87837 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.033 / Rsym value: 0.033 / Net I/σ(I): 29.5 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.098 / Mean I/σ(I) obs: 6.4 / Num. unique all: 7649 / Rsym value: 0.098 / % possible all: 81.9 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1b6s Resolution: 1.6→30 Å / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 99.85 Å2 / Biso mean: 27.439 Å2 / Biso min: 6.97 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→30 Å
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