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Yorodumi- PDB-7y94: Crystal structure of Escherichia coli Adenine Phosphoribosyltrans... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7y94 | ||||||
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Title | Crystal structure of Escherichia coli Adenine Phosphoribosyltransferase (APRT) in complex with Adenine | ||||||
Components | Adenine phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / Adenine Phosphoribosyltransferase / Substrate Complex / Escherichia coli / Purine Salvage Pathway / Nucleotide Metabolism | ||||||
Function / homology | Function and homology information adenine salvage / adenine phosphoribosyltransferase activity / adenine phosphoribosyltransferase / AMP salvage / purine ribonucleoside salvage / magnesium ion binding / protein homodimerization activity / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Yadav, P. / Kushwaha, G.S. / Bhavesh, N.S. | ||||||
Funding support | India, 1items
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Citation | Journal: To Be Published Title: Crystal structure of Escherichia coli Adenine Phosphoribosyltransferase (APRT) in complex with Adenine Authors: Yadav, P. / Kushwaha, G.S. / Bhavesh, N.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7y94.cif.gz | 94 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7y94.ent.gz | 69.3 KB | Display | PDB format |
PDBx/mmJSON format | 7y94.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7y94_validation.pdf.gz | 1017.2 KB | Display | wwPDB validaton report |
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Full document | 7y94_full_validation.pdf.gz | 1017.9 KB | Display | |
Data in XML | 7y94_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 7y94_validation.cif.gz | 29.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y9/7y94 ftp://data.pdbj.org/pub/pdb/validation_reports/y9/7y94 | HTTPS FTP |
-Related structure data
Related structure data | 2dy0S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 20163.100 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: apt, b0469, JW0458 / Production host: Escherichia coli (E. coli) References: UniProt: P69503, adenine phosphoribosyltransferase |
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-Non-polymers , 6 types, 396 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | #6: Chemical | ChemComp-EDO / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.68 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100 mM Tris-HCl pH 8.0, 20 % PEG 4000, 0.2 M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 21, 2022 / Details: Toroidal mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 |
Reflection | Resolution: 1.498→41.63 Å / Num. obs: 54573 / % possible obs: 99.8 % / Redundancy: 5.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.034 / Rrim(I) all: 0.078 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.498→1.524 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.727 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2710 / CC1/2: 0.812 / Rpim(I) all: 0.342 / Rrim(I) all: 0.805 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DY0 Resolution: 1.5→41.63 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.617 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.831 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→41.63 Å
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Refine LS restraints |
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