+Open data
-Basic information
Entry | Database: PDB / ID: 4o7t | ||||||
---|---|---|---|---|---|---|---|
Title | SAICAR synthetase (Type-2) in complex with ADP, ASP and TMP | ||||||
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 Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å | ||||||
Authors | Manjunath, K. / Jeyakanthan, J. / Sekar, K. | ||||||
Citation | Journal: To be Published Title: SAICAR synthetase (Type-2) in complex with ADP, ASP and TMP Authors: Manjunath, K. / Jeyakanthan, J. / Sekar, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4o7t.cif.gz | 64.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4o7t.ent.gz | 45.1 KB | Display | PDB format |
PDBx/mmJSON format | 4o7t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/4o7t ftp://data.pdbj.org/pub/pdb/validation_reports/o7/4o7t | HTTPS FTP |
---|
-Related structure data
Related structure data | 3u55S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-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 |
---|
-Non-polymers , 5 types, 108 molecules
#2: Chemical | ChemComp-TMP / | ||
---|---|---|---|
#3: Chemical | ChemComp-ADP / | ||
#4: Chemical | ChemComp-ASP / | ||
#5: Chemical | #6: 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: 49.6 % / Mosaicity: 0.64 ° |
---|---|
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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 27, 2012 / 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 | Redundancy: 7.7 % / Av σ(I) over netI: 15 / Number: 120337 / Rsym value: 0.041 / D res high: 2.1 Å / D res low: 77.645 Å / Num. obs: 15546 / % possible obs: 96.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→42.49 Å / Num. obs: 15546 / % possible obs: 96.6 % / Redundancy: 7.7 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 35.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.135 / Mean I/σ(I) obs: 13.9 / Num. unique all: 17000 / % possible all: 94.5 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Model details: Phaser MODE: MR_AUTO
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3U55 Resolution: 2.1→42.49 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.914 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.846 / SU B: 4.493 / SU ML: 0.119 / SU R Cruickshank DPI: 0.229 / SU Rfree: 0.1856 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||
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: 61.46 Å2 / Biso mean: 23.7 Å2 / Biso min: 8.56 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→42.49 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
|