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- PDB-2r7k: Crystal structure of FAICAR synthetase (PurP) from M. jannaschii ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2r7k | ||||||
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Title | Crystal structure of FAICAR synthetase (PurP) from M. jannaschii complexed with AMPPCP and AICAR | ||||||
![]() | 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase | ||||||
![]() | LIGASE / ATP-grasp superfamily / ATP-binding / Magnesium / Manganese / Metal-binding / Nucleotide-binding | ||||||
Function / homology | ![]() formate-phosphoribosylaminoimidazolecarboxamide ligase / ligase activity, forming carbon-nitrogen bonds / 'de novo' IMP biosynthetic process / magnesium ion binding / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, Y. / White, R.H. / Ealick, S.E. | ||||||
![]() | ![]() Title: Crystal structure and function of 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase from Methanocaldococcus jannaschii. Authors: Zhang, Y. / White, R.H. / Ealick, S.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89.9 KB | Display | ![]() |
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PDB format | ![]() | 67.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 16.4 KB | Display | |
Data in CIF | ![]() | 22.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2r7lC ![]() 2r7mC ![]() 2r7nC ![]() 2r84C ![]() 2r85C ![]() 2r86C ![]() 2r87C 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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Unit cell |
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Components on special symmetry positions |
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Details | biological unit is a hexamer from the monomer in the asymmetric unit by the operations: (x,y,z), (-y,x-y,z), (-x+y,-x,z), (y,x,-z), (x-y,-y,-z), (-x,-x+y,-z) |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 40873.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: purP / Cell line (production host): B834(DE3) / Production host: ![]() ![]() References: UniProt: Q57600, Ligases; Forming carbon-nitrogen bonds; Other carbon-nitrogen ligases |
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-Non-polymers , 5 types, 113 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/ACP.gif)
![](data/chem/img/AMZ.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/ACP.gif)
![](data/chem/img/AMZ.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-ACP / | #5: Chemical | ChemComp-AMZ / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.61 Å3/Da / Density % sol: 65.92 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.1 Details: 1.2 M (NH4)2SO4, 0.2 M NaCl, 0.1 M Na acetate, pH 4.1, vapor diffusion, hanging drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 5, 2006 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 19.6 % / Av σ(I) over netI: 12.7 / Number: 401282 / Rmerge(I) obs: 0.097 / Χ2: 1.54 / D res high: 2.5 Å / D res low: 50 Å / Num. obs: 20490 / % possible obs: 98 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.1→50 Å / Num. all: 34334 / Num. obs: 34235 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16.2 % / Rmerge(I) obs: 0.079 / Χ2: 1.712 / Net I/σ(I): 21.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.28 / Num. unique all: 3125 / Χ2: 1.433 / % possible all: 90.7 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]()
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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 mean: 48.062 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→46.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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