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Yorodumi- PDB-5k7x: Fully ligated Adenylosuccinate Synthetase from Pyrococcus horikos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5k7x | ||||||
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Title | Fully ligated Adenylosuccinate Synthetase from Pyrococcus horikoshii OT3 with GTP, IMP and Hadacidin | ||||||
Components | Adenylosuccinate synthetase | ||||||
Keywords | LIGASE / Adenylosuccinate synthetase / Pyrococcus horikoshii OT3 / GTP / IMP / Hadacidin | ||||||
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 | Pyrococcus horikoshii OT3 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.803 Å | ||||||
Authors | Xie, Y. / Cheng, Z. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Crystal structure of hypothetical adenylosuccinate synthetase, PH0438 from Pyrococcus horikoshii OT3 Authors: Xie, Y. / Kishisita, S. / Murayama, K. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5k7x.cif.gz | 801.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5k7x.ent.gz | 669 KB | Display | PDB format |
PDBx/mmJSON format | 5k7x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5k7x_validation.pdf.gz | 3.9 MB | Display | wwPDB validaton report |
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Full document | 5k7x_full_validation.pdf.gz | 4 MB | Display | |
Data in XML | 5k7x_validation.xml.gz | 80.6 KB | Display | |
Data in CIF | 5k7x_validation.cif.gz | 103 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k7/5k7x ftp://data.pdbj.org/pub/pdb/validation_reports/k7/5k7x | HTTPS FTP |
-Related structure data
Related structure data | 2d7uSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 37418.543 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii OT3 (archaea) / Strain: OT3 / Gene: purA, PH0438 / Plasmid: pET19b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O58187, adenylosuccinate synthase |
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-Non-polymers , 5 types, 82 molecules
#2: Chemical | ChemComp-GTP / #3: Chemical | ChemComp-IMP / #4: Chemical | ChemComp-HDA / #5: Chemical | ChemComp-MG / #6: Water | ChemComp-HOH / | |
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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: 2.6 Å3/Da / Density % sol: 52.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: MES, PEG550 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 21, 2016 / Details: Silicon |
Radiation | Monochromator: Zr filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 55976 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 1.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2D7U Resolution: 2.803→39.123 Å / SU ML: 0.36 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 27.34 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.803→39.123 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -10.1182 Å / Origin y: 30.2758 Å / Origin z: -34.7333 Å
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Refinement TLS group | Selection details: all |