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Yorodumi- PDB-1p9b: Structure of fully ligated Adenylosuccinate synthetase from Plasm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1p9b | ||||||
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Title | Structure of fully ligated Adenylosuccinate synthetase from Plasmodium falciparum | ||||||
Components | Adenylosuccinate Synthetase | ||||||
Keywords | LIGASE | ||||||
Function / homology | Function and homology information adenylosuccinate synthase / adenylosuccinate synthase activity / 'de novo' AMP biosynthetic process / GTP binding / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Eaazhisai, K. / Jayalakshmi, R. / Gayathri, P. / Anand, R.P. / Sumathy, K. / Balaram, H. / Murthy, M.R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Crystal Structure of Fully Ligated Adenylosuccinate Synthetase from Plasmodium falciparum. Authors: Eaazhisai, K. / Jayalakshmi, R. / Gayathri, P. / Anand, R.P. / Sumathy, K. / Balaram, H. / Murthy, M.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p9b.cif.gz | 107.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p9b.ent.gz | 79.7 KB | Display | PDB format |
PDBx/mmJSON format | 1p9b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1p9b_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1p9b_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1p9b_validation.xml.gz | 21 KB | Display | |
Data in CIF | 1p9b_validation.cif.gz | 30.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/1p9b ftp://data.pdbj.org/pub/pdb/validation_reports/p9/1p9b | HTTPS FTP |
-Related structure data
Related structure data | 1cibS 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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Details | The second part of the biological assembly is generated by the two fold axis: -X,Y,1/2-Z |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 50088.738 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Plasmid: pET23d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9U8D3, adenylosuccinate synthase |
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-Non-polymers , 6 types, 283 molecules
#2: Chemical | ChemComp-MG / |
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#3: Chemical | ChemComp-NO3 / |
#4: Chemical | ChemComp-IMO / |
#5: Chemical | ChemComp-HDA / |
#6: Chemical | ChemComp-GDP / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.49 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: liquid diffusion / pH: 6.5 Details: PEG4000, Sodium cacodylate, pH 6.5, LIQUID DIFFUSION, temperature 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 10, 2003 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→32.91 Å / Num. all: 164288 / Num. obs: 28913 / Redundancy: 5.7 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.068 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2833 / Rsym value: 0.36 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 29594 / % possible obs: 97.8 % / Num. measured all: 358593 / Rmerge(I) obs: 0.068 |
Reflection shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.07 Å / % possible obs: 97.1 % / Rmerge(I) obs: 0.363 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CIB Resolution: 2→32.91 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 25.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→32.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.025
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 50 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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