+Open data
-Basic information
Entry | Database: PDB / ID: 4o7v | ||||||
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Title | SAICAR synthetase (Type-2) in complex with ADP and UDP/UMP | ||||||
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: 2.3 Å | ||||||
Authors | Manjunath, K. / Jeyakanthan, J. / Sekar, K. | ||||||
Citation | Journal: To be Published Title: SAICAR synthetase (Type-2) in complex with ADP and UDP/UMP 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 | 4o7v.cif.gz | 65.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4o7v.ent.gz | 46 KB | Display | PDB format |
PDBx/mmJSON format | 4o7v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/4o7v ftp://data.pdbj.org/pub/pdb/validation_reports/o7/4o7v | HTTPS FTP |
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-Related structure data
Related structure data | 3u55S 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 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 , 6 types, 99 molecules
#2: Chemical | ChemComp-UDP / |
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#3: Chemical | ChemComp-ADP / |
#4: Chemical | ChemComp-U5P / |
#5: Chemical | ChemComp-ACT / |
#6: Chemical | ChemComp-PO4 / |
#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: 2.44 Å3/Da / Density % sol: 49.59 % / Mosaicity: 1.44 ° |
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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: Nov 24, 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: 6.2 % / Av σ(I) over netI: 10 / Number: 76276 / Rsym value: 0.073 / D res high: 1.897 Å / D res low: 77.56 Å / Num. obs: 12230 / % possible obs: 99.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.3→55.1 Å / Num. obs: 12230 / % possible obs: 99.2 % / Redundancy: 6.2 % / Biso Wilson estimate: 27.1 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 20.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 7.1 / Num. unique all: 10205 / % possible all: 98.5 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3U55 Resolution: 2.3→55.1 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.889 / WRfactor Rfree: 0.2176 / WRfactor Rwork: 0.1685 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8396 / SU B: 6.611 / SU ML: 0.163 / SU R Cruickshank DPI: 0.3413 / SU Rfree: 0.2437 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.341 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
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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: 72.53 Å2 / Biso mean: 22.955 Å2 / Biso min: 5.05 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→55.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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