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Yorodumi- PDB-4nye: Structures of SAICAR Synthetase (PurC) from Streptococcus pneumon... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nye | ||||||
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Title | Structures of SAICAR Synthetase (PurC) from Streptococcus pneumoniae with ADP, Mg2+, AIR and L-Asp | ||||||
Components | Phosphoribosylaminoimidazole-succinocarboxamide synthase | ||||||
Keywords | LIGASE / SAICAR synthetase / alpha/beta / CAIR / L-Asp Mg2+ / NONE | ||||||
Function / homology | Function and homology information phosphoribosylaminoimidazolesuccinocarboxamide synthase / phosphoribosylaminoimidazolesuccinocarboxamide synthase activity / cobalamin biosynthetic process / 'de novo' IMP biosynthetic process / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å | ||||||
Authors | Fung, L.W.-M. / Johnson, M.E. / Abad-Zapatero, C. / Wolf, N.M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structures of SAICAR synthetase (PurC) from Streptococcus pneumoniae with ADP, Mg(2+), AIR and Asp. Authors: Wolf, N.M. / Abad-Zapatero, C. / Johnson, M.E. / Fung, L.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nye.cif.gz | 113.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nye.ent.gz | 85.8 KB | Display | PDB format |
PDBx/mmJSON format | 4nye.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nye_validation.pdf.gz | 1022 KB | Display | wwPDB validaton report |
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Full document | 4nye_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4nye_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 4nye_validation.cif.gz | 32.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ny/4nye ftp://data.pdbj.org/pub/pdb/validation_reports/ny/4nye | HTTPS FTP |
-Related structure data
Related structure data | 4fe2C 2gqrS C: citing same article (ref.) 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 29208.057 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: ATCC BAA-334 / TIGR4 / Gene: purC, SP_0044 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-GOLD References: UniProt: Q07296, phosphoribosylaminoimidazolesuccinocarboxamide synthase |
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-Non-polymers , 5 types, 168 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / | #5: Chemical | #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: 2.2 Å3/Da / Density % sol: 43.99 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 40% PEG 200, 0.2 M sodium acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 13, 2011 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.69→40.44 Å / Num. all: 11902 / Num. obs: 10808 / % possible obs: 82.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.69→2.74 Å / % possible all: 69.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2GQR Resolution: 2.69→40.44 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.851 / SU B: 17.765 / SU ML: 0.376 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R Free: 0.541 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 43.136 Å2
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Refinement step | Cycle: LAST / Resolution: 2.69→40.44 Å
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Refine LS restraints |
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