[English] 日本語
Yorodumi- PDB-3u55: Crystal structure (Type-2) of SAICAR synthetase from Pyrococcus h... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3u55 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure (Type-2) of SAICAR synthetase from Pyrococcus horikoshii OT3 | ||||||
Components | Phosphoribosylaminoimidazole-succinocarboxamide synthase | ||||||
Keywords | LIGASE / SAICAR synthetase-like fold / ATP-binding / Phosphoribosylaminoimidazole-succinocarboxamide synthetase / PurC / De novo purine biosynthesis / Ligation of carboxy and amine groups | ||||||
Function / homology | Function and homology information phosphoribosylaminoimidazolesuccinocarboxamide synthase / phosphoribosylaminoimidazolesuccinocarboxamide synthase activity / cobalamin biosynthetic process / 'de novo' IMP biosynthetic process / ATP binding Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Manjunath, K. / Kanaujia, S.P. / Kanagaraj, S. / Jeyakanthan, J. / Sekar, K. | ||||||
Citation | Journal: Int.J.Biol.Macromol. / Year: 2013 Title: Structure of SAICAR synthetase from Pyrococcus horikoshii OT3: insights into thermal stability Authors: Manjunath, K. / Kanaujia, S.P. / Kanagaraj, S. / Jeyakanthan, J. / Sekar, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3u55.cif.gz | 64.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3u55.ent.gz | 47 KB | Display | PDB format |
PDBx/mmJSON format | 3u55.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u5/3u55 ftp://data.pdbj.org/pub/pdb/validation_reports/u5/3u55 | HTTPS FTP |
---|
-Related structure data
Related structure data | 3u54SC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
| |||||||||
Details | AUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN |
-Components
#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 | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.64 % |
---|---|
Crystal grow | Temperature: 293 K / Method: microbatch underoil / pH: 4.6 Details: 0.2M AMMONIUM SULPHATE, 0.1M SODIUM ACETATE TRIHYDRATE, 30% PEG MONOMETHYL ETHER, pH 4.6, MICROBATCH UNDEROIL, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 10, 2011 / 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: 1.9→42.42 Å / Num. obs: 21450 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 24.1 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 8 / Num. unique all: 3041 / % possible all: 97.5 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3U54 Resolution: 1.9→42.42 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.884 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.825 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→42.42 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
|