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Yorodumi- PDB-3u54: Crystal structure (Type-1) of SAICAR synthetase from Pyrococcus h... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3u54 | ||||||
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Title | Crystal structure (Type-1) 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: 2.35 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3u54.cif.gz | 108.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3u54.ent.gz | 82.3 KB | Display | PDB format |
PDBx/mmJSON format | 3u54.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u5/3u54 ftp://data.pdbj.org/pub/pdb/validation_reports/u5/3u54 | HTTPS FTP |
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-Related structure data
Related structure data | 3u55C 2yzlS 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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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 1 / Auth seq-ID: 12 - 233 / Label seq-ID: 12 - 233
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Details | AUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 27714.535 Da / Num. of mol.: 2 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, 183 molecules
#2: Chemical | ChemComp-BU1 / | ||||||
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#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-CD / #5: Chemical | ChemComp-ACT / | #6: 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: 2.35 Å3/Da / Density % sol: 47.64 % |
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Crystal grow | Temperature: 293 K / Method: microbatch underoil / pH: 7.5 Details: 0.05M cadmium sulfate hydrate, 0.1M HEPES buffer, 1.0M sodium acetate trihydrate, 40%(w/v) 1,4-butanediol, pH 7.5, 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: Aug 15, 2010 / 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: 2.35→55.26 Å / Num. obs: 21057 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 33.1 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.35→2.48 Å / Redundancy: 4 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YZL Resolution: 2.35→55.26 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.838 / SU B: 8.865 / SU ML: 0.22 / Cross valid method: THROUGHOUT / ESU R: 0.485 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 24.812 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→55.26 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1719 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.35→2.411 Å / Total num. of bins used: 20
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