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- PDB-6d9r: The substrate-bound crystal structure of HPRT (hypoxanthine phosp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6d9r | ||||||||||||
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Title | The substrate-bound crystal structure of HPRT (hypoxanthine phosphoribosyltransferase) | ||||||||||||
![]() | Hypoxanthine phosphoribosyltransferase | ||||||||||||
![]() | TRANSFERASE / HPRT / hypoxanthine phosphoribosyltransferase | ||||||||||||
Function / homology | ![]() hypoxanthine phosphoribosyltransferase / guanine salvage / hypoxanthine metabolic process / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / purine ribonucleoside salvage / nucleotide binding / magnesium ion binding ...hypoxanthine phosphoribosyltransferase / guanine salvage / hypoxanthine metabolic process / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / purine ribonucleoside salvage / nucleotide binding / magnesium ion binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Satyshur, K.A. / Wolak, C. / Anderson, B. / Dubiel, K. / Keck, J.L. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Evolution of (p)ppGpp-HPRT regulation through diversification of an allosteric oligomeric interaction. Authors: Anderson, B.W. / Liu, K. / Wolak, C. / Dubiel, K. / She, F. / Satyshur, K.A. / Keck, J.L. / Wang, J.D. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 164.2 KB | Display | ![]() |
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PDB format | ![]() | 131.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 20.6 KB | Display | |
Data in CIF | ![]() | 29.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6d9qC ![]() 6d9sSC 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 on special symmetry positions |
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Components
-Protein / Sugars , 2 types, 4 molecules AB![](data/chem/img/PRP.gif)
![](data/chem/img/PRP.gif)
#1: Protein | Mass: 20503.646 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: hpt, hprT, hpt1, tilS, BA_0063, A9486_05730, ABW01_27435, BASH2_00187, BVG01_28865, CN272_24955, CN488_12230, CN504_22375, COE56_22980, COJ30_24475, COK92_19380, COL95_25280, MCCC1A01412_27610 Plasmid: pLIC trPC-HA / Production host: ![]() ![]() References: UniProt: A0A1S0QLD4, UniProt: B9ZW32*PLUS, hypoxanthine phosphoribosyltransferase #3: Sugar | |
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-Non-polymers , 6 types, 342 molecules ![](data/chem/img/9DG.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-PEG / #6: Chemical | #7: Chemical | ChemComp-EDO / #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M ammonium acetate, 0.1 M sodium acetate trihydrate, pH 4.6, 30% PEG4000 PH range: 4.6 - 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Mar 8, 2017 |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→40.167 Å / Num. obs: 51750 / % possible obs: 99.8 % / Redundancy: 21.5 % / Biso Wilson estimate: 19.34 Å2 / Rpim(I) all: 0.029 / Rrim(I) all: 0.137 / Net I/σ(I): 31.09 |
Reflection shell | Resolution: 1.64→1.67 Å / Redundancy: 14.4 % / Num. unique obs: 2548 / CC1/2: 0.81 / Rpim(I) all: 0.35 / Rrim(I) all: 1.376 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 6D9S Resolution: 1.64→37.19 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.44
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.64→37.19 Å
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Refine LS restraints |
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LS refinement shell |
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