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Yorodumi- PDB-6lbp: Structure of the Glutamine Phosphoribosylpyrophosphate Amidotrans... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lbp | ||||||
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Title | Structure of the Glutamine Phosphoribosylpyrophosphate Amidotransferase from Arabidopsis thaliana | ||||||
Components | Amidophosphoribosyltransferase 2, chloroplastic | ||||||
Keywords | TRANSFERASE / Amidotransferase / tetramer | ||||||
Function / homology | Function and homology information plastid stroma / amidophosphoribosyltransferase / amidophosphoribosyltransferase activity / chloroplast organization / purine nucleobase biosynthetic process / nucleoside metabolic process / purine nucleotide biosynthetic process / 'de novo' IMP biosynthetic process / chloroplast stroma / glutamine metabolic process ...plastid stroma / amidophosphoribosyltransferase / amidophosphoribosyltransferase activity / chloroplast organization / purine nucleobase biosynthetic process / nucleoside metabolic process / purine nucleotide biosynthetic process / 'de novo' IMP biosynthetic process / chloroplast stroma / glutamine metabolic process / iron-sulfur cluster binding / chloroplast / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.065 Å | ||||||
Authors | Yi, Z. / Cao, X. / Han, F. / Feng, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Front Plant Sci / Year: 2020 Title: Crystal Structure of the Chloroplastic Glutamine Phosphoribosylpyrophosphate Amidotransferase GPRAT2 FromArabidopsis thaliana. Authors: Cao, X. / Du, B. / Han, F. / Zhou, Y. / Ren, J. / Wang, W. / Chen, Z. / Zhang, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lbp.cif.gz | 188.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lbp.ent.gz | 147.7 KB | Display | PDB format |
PDBx/mmJSON format | 6lbp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lbp_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 6lbp_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 6lbp_validation.xml.gz | 33.1 KB | Display | |
Data in CIF | 6lbp_validation.cif.gz | 45.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lb/6lbp ftp://data.pdbj.org/pub/pdb/validation_reports/lb/6lbp | HTTPS FTP |
-Related structure data
Related structure data | 1gphS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: SF4 / End label comp-ID: SF4 / Auth seq-ID: 87 - 600 / Label seq-ID: 13
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-Components
#1: Protein | Mass: 53342.559 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ASE2, CIA1, DOV1, GPRAT2, PURF2, At4g34740, T4L20.320 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9STG9, amidophosphoribosyltransferase #2: Chemical | Has ligand of interest | Y | |
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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: 4.98 Å3/Da / Density % sol: 75.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1 M Sodium citrate tribasic pH 5.6, 1.0 M Ammonium phosphate monobasic |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Jan 5, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.065→36.656 Å / Num. obs: 38107 / % possible obs: 99.03 % / Redundancy: 6 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 18.25 |
Reflection shell | Resolution: 3.065→3.175 Å / Rmerge(I) obs: 0.732 / Mean I/σ(I) obs: 3.11 / Num. unique obs: 3526 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GPH Resolution: 3.065→36.656 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0.57 / Phase error: 22.67
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 131 Å2 / Biso mean: 59.2485 Å2 / Biso min: 29.72 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.065→36.656 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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