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Yorodumi- PDB-6zxq: Adenylosuccinate Synthetase from H. pylori in complex with HDA, G... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zxq | ||||||
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Title | Adenylosuccinate Synthetase from H. pylori in complex with HDA, GDP, IMO, Mg | ||||||
Components | Adenylosuccinate synthetaseAdenylosuccinate synthase | ||||||
Keywords | LIGASE / Complex / Synthetase / N-C Ligase / Purine salvage pathway | ||||||
Function / homology | Function and homology information adenylosuccinate synthase / adenylosuccinate synthase activity / IMP metabolic process / 'de novo' AMP biosynthetic process / GTP binding / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Helicobacter pylori 26695 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Bubic, A. / Stefanic, Z. | ||||||
Funding support | Croatia, 1items
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Citation | Journal: Int.J.Biol.Macromol. / Year: 2023 Title: The pursuit of new alternative ways to eradicate Helicobacter pylori continues: Detailed characterization of interactions in the adenylosuccinate synthetase active site Authors: Bubic, A. / Narczyk, M. / Petek, A. / Wojtys, M.I. / Maksymiuk, W. / Wielgus-Kutrowska, B. / Winiewska-Szajewska, M. / Pavkov-Keller, T. / Bertosa, B. / Stefanic, Z. / Luic, M. / Bzowska, A. / Lescic Asler, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zxq.cif.gz | 196.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zxq.ent.gz | 151.5 KB | Display | PDB format |
PDBx/mmJSON format | 6zxq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zx/6zxq ftp://data.pdbj.org/pub/pdb/validation_reports/zx/6zxq | HTTPS FTP |
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-Related structure data
Related structure data | 3r7tS S: Starting model for refinement |
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Similar structure data |
-Links
-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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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 46880.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Gene: purA, HP_0255 / Plasmid: pET21b(+) / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): BL-21(DE3) RIL / References: UniProt: P56137, adenylosuccinate synthase |
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-Non-polymers , 5 types, 458 molecules
#2: Chemical | ChemComp-HDA / |
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#3: Chemical | ChemComp-GDP / |
#4: Chemical | ChemComp-IMO / |
#5: Chemical | ChemComp-MG / |
#6: Water | ChemComp-HOH / |
-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: 2.66 Å3/Da / Density % sol: 53.78 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: Ammonium sulfate, Tris , PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033195 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 10, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.033195 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.4→48.46 Å / Num. obs: 93653 / % possible obs: 98.5 % / Redundancy: 6.58 % / Biso Wilson estimate: 23.066 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.134 / Rrim(I) all: 0.145 / Χ2: 0.972 / Net I/σ(I): 8.09 / Num. measured all: 616201 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3r7t Resolution: 1.4→48.46 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.16 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 133.75 Å2 / Biso mean: 26.3089 Å2 / Biso min: 11.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.4→48.46 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15
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