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- PDB-3mbi: Crystal structure of the phosphoribosylpyrophosphate (PRPP) synth... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3mbi | |||||||||
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Title | Crystal structure of the phosphoribosylpyrophosphate (PRPP) synthetase from Thermoplasma volcanium in complex with ADP-Mg2+ and ribose 5-phosphate | |||||||||
![]() | Ribose-phosphate pyrophosphokinase | |||||||||
![]() | TRANSFERASE / Phosphoribosyl transferase / ATP analog binding / Ribose 5-phosphate 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, L.T. / Cherney, M.M. / 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. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 265.2 KB | Display | ![]() |
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PDB format | ![]() | 211.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 55.5 KB | Display | |
Data in CIF | ![]() | 81.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3lpnSC ![]() 3lrtC ![]() 3nagC 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein / Sugars , 2 types, 5 molecules ABCD![](data/chem/img/HSX.gif)
![](data/chem/img/HSX.gif)
#1: Protein | Mass: 32294.492 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q97CA5, ribose-phosphate diphosphokinase #5: Sugar | ChemComp-HSX / | |
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-Non-polymers , 4 types, 1265 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-ADP / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.97 % |
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Crystal grow | Temperature: 293 K / pH: 7.5 Details: 30% PEG600, 0.1M HEPES, 10% MPD, 0.1% LDAO, pH 7.5, 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: 1.797→25.471 Å / Num. obs: 105923 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.71 / % possible all: 96.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3LPN Resolution: 1.8→25.47 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 22.81 / 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: 39.23 Å2 / ksol: 0.33 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→25.47 Å
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Refine LS restraints |
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LS refinement shell |
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