+Open data
-Basic information
Entry | Database: PDB / ID: 4o7n | ||||||
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Title | SAICAR synthetase (Type-2) in complex with ADP | ||||||
Components | Phosphoribosylaminoimidazole-succinocarboxamide synthase | ||||||
Keywords | LIGASE / SAICAR Synthetase-like fold / ATP binding / CAIR binding / Aspartate binding | ||||||
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 | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.16 Å | ||||||
Authors | Manjunath, K. / Jeyakanthan, J. / Sekar, K. | ||||||
Citation | Journal: To be Published Title: SAICAR synthetase (Type-2) in complex with ADP Authors: Manjunath, K. / Jeyakanthan, J. / Sekar, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4o7n.cif.gz | 63.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4o7n.ent.gz | 45.4 KB | Display | PDB format |
PDBx/mmJSON format | 4o7n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/4o7n ftp://data.pdbj.org/pub/pdb/validation_reports/o7/4o7n | HTTPS FTP |
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-Related structure data
Related structure data | 4o7lC 3u55S 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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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: 27480.061 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH0239, purC / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL References: UniProt: O57978, phosphoribosylaminoimidazolesuccinocarboxamide synthase |
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-Non-polymers , 5 types, 82 molecules
#2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-ADP / | #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: 2.43 Å3/Da / Density % sol: 49.39 % |
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Crystal grow | Temperature: 293 K / Method: microbatch underoil / pH: 4.6 Details: 0.2M Ammonium Sulphate, 0.1M Sodium acetate trihydrate, 30% w/v PEG monomethyl ether 2000, pH 4.6, Microbatch Underoil, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 1, 2013 / Details: Mirrors |
Radiation | Monochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.16→55.03 Å / Num. obs: 14847 / % possible obs: 100 % / Redundancy: 5 % / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2.16→2.28 Å / Redundancy: 5 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 6.2 / Num. unique all: 10478 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3U55 Resolution: 2.16→55.03 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.915 / SU B: 5.369 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.253 / ESU R Free: 0.205 / 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 max: 70.65 Å2 / Biso mean: 26.576 Å2 / Biso min: 11.43 Å2
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Refinement step | Cycle: LAST / Resolution: 2.16→55.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.16→2.216 Å / Total num. of bins used: 20
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