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- PDB-3lrt: Crystal structure of the phosphoribosyl pyrophosphate (PRPP) synt... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3lrt | ||||||
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Title | Crystal structure of the phosphoribosyl pyrophosphate (PRPP) synthetase from Thermoplasma volcanium in complex with ADP. | ||||||
![]() | Ribose-phosphate pyrophosphokinase | ||||||
![]() | TRANSFERASE / Phosphoribosyl transferase / ATP analog binding / ATP-binding / Kinase / Metal-binding / Nucleotide biosynthesis / Nucleotide-binding | ||||||
Function / homology | ![]() ribose phosphate diphosphokinase complex / ribose-phosphate diphosphokinase / ribose phosphate diphosphokinase activity / ribonucleoside monophosphate biosynthetic process / 5-phosphoribose 1-diphosphate biosynthetic process / purine nucleotide biosynthetic process / kinase activity / phosphorylation / magnesium ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cherney, M.M. / Cherney, L.T. / Garen, C.R. / James, M.N.G. | ||||||
![]() | ![]() Title: The structures of Thermoplasma volcanium phosphoribosyl pyrophosphate synthetase bound to ribose-5-phosphate and ATP analogs. Authors: Cherney, M.M. / Cherney, L.T. / Garen, C.R. / James, M.N. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135.8 KB | Display | ![]() |
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PDB format | ![]() | 105.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 27.4 KB | Display | |
Data in CIF | ![]() | 39.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3lpnSC ![]() 3mbiC ![]() 3nagC 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: 32221.441 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q97CA5, ribose-phosphate diphosphokinase #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 2M ammonium sulfate, 0.1 M sodium citrate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 25, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→50 Å / Num. all: 79457 / Num. obs: 71194 / % possible obs: 89.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.53→1.58 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 1.6 / Num. unique all: 4586 / Rsym value: 0.418 / % possible all: 58.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3LPN Resolution: 1.534→24.62 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0.03 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.061 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.534→24.62 Å
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Refine LS restraints |
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LS refinement shell |
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