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- PDB-3k5i: Crystal structure of N5-carboxyaminoimidazole synthase from asper... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3k5i | |||||||||
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Title | Crystal structure of N5-carboxyaminoimidazole synthase from aspergillus clavatus in complex with ADP and 5-aminoimadazole ribonucleotide | |||||||||
![]() | Phosphoribosyl-aminoimidazole carboxylase | |||||||||
![]() | LYASE / purine biosynthesis / ATP-grasp | |||||||||
Function / homology | ![]() phosphoribosylaminoimidazole carboxylase / : / phosphoribosylaminoimidazole carboxylase activity / 'de novo' IMP biosynthetic process / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Thoden, J.B. / Holden, H.M. / Paritala, H. / Firestine, S.M. | |||||||||
![]() | ![]() Title: Structural and functional studies of Aspergillus clavatus N(5)-carboxyaminoimidazole ribonucleotide synthetase Authors: Thoden, J.B. / Holden, H.M. / Paritala, H. / 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 | ![]() | 337.8 KB | Display | ![]() |
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PDB format | ![]() | 269.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3k5hSC 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 44727.789 Da / Num. of mol.: 4 / Fragment: residues 1-383 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A1CII2, phosphoribosylaminoimidazole carboxylase |
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-Non-polymers , 6 types, 1145 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/NHE.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/AIR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NHE.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/AIR.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NA / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-ADP / #5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-AIR / #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.81 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 20% PEG-5000 monomethylether, 40 mM MgCl2, 200 mM NaCl, 100 mM CHES, 10 mM ATP, 10 mM 5-aminoimidazole ribonucleotide, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Jan 27, 2009 / Details: montel |
Radiation | Monochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 118616 / Num. obs: 118616 / % possible obs: 91.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 2 / Num. unique all: 15717 / Rsym value: 0.286 / % possible all: 86.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB 3K5H Resolution: 2→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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