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Yorodumi- PDB-6ils: Structure of Arabidopsis thaliana Ribokinase complexed with Ribos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ils | |||||||||
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Title | Structure of Arabidopsis thaliana Ribokinase complexed with Ribose and ATP | |||||||||
Components | Ribokinase | |||||||||
Keywords | TRANSFERASE / Ribose / Ribokinase / AtRBSK / PfkB family / Phosphotransferase | |||||||||
Function / homology | Function and homology information plastid nucleoid / chloroplast nucleoid / ribokinase / ribokinase activity / D-ribose catabolic process / nucleoside metabolic process / chloroplast stroma / chloroplast / ATP binding / metal ion binding / nucleus Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Kang, P. / Oh, J. / Rhee, S. | |||||||||
Funding support | Korea, Republic Of, 2items
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Citation | Journal: J. Struct. Biol. / Year: 2019 Title: Crystal structure and mutational analyses of ribokinase from Arabidopsis thaliana. Authors: Kang, P.A. / Oh, J. / Lee, H. / Witte, C.P. / Rhee, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ils.cif.gz | 139.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ils.ent.gz | 107.1 KB | Display | PDB format |
PDBx/mmJSON format | 6ils.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/il/6ils ftp://data.pdbj.org/pub/pdb/validation_reports/il/6ils | HTTPS FTP |
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-Related structure data
Related structure data | 6ilrSC 6iltC S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 32928.902 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: To make AtRBSK crystal, we deleted 1-67 residues of AtRBSK. The reason for target protein truncation is to remove the disorder. Miss matched sequence Met67 is expression tag. The full-length ...Details: To make AtRBSK crystal, we deleted 1-67 residues of AtRBSK. The reason for target protein truncation is to remove the disorder. Miss matched sequence Met67 is expression tag. The full-length AtRBSK sequence is as follows : >ribokinase.at MMKGISSVSQSINYNPYIEFNRPQLQISTVNPNPAQSRFSRPRSLRVLSLSADPSANRNPKSAVDAHAPPLVVVGSANADIYVEIERLPKEGETISAKTGQTLAGGKGANQAACGAKLMYPTYFVGRLGEDAHGKLIAEALGDDGCGVHLDYVRSVNNEPTGHAVVMLQSDGQNSIIIVGGANMKAWPEIMSDDDLEIVRNAGIVLLQREIPDSINIQVAKAVKKAGVPVILDVGGMDTPIPNELLDSIDILSPNETELSRLTGMPTETFEQISQAVAKCHKLGVKQVLVKLGSKGSALFIQGEKPIQQSIIPAAQVVDTTGAGDTFTAAFAVAMVEGKSHEECLRFAAAAASLCVQVKGAIPSMPDRKSVLKLLKFSI Therefore, N-terminal residues 1-67 were deleted to make AtRBSK crystal. Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g17160, F20D23.14, F20D23_14 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A1A6H3, ribokinase #2: Chemical | #3: Chemical | #4: Sugar | ChemComp-RIB / | #5: Water | ChemComp-HOH / | |
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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: 3.11 Å3/Da / Density % sol: 60.47 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1M sodium citrate (pH 5.5) , 40% (v/v) PEG 600 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. obs: 84606 / % possible obs: 99.8 % / Redundancy: 13.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Net I/σ(I): 29.6 |
Reflection shell | Resolution: 1.75→1.81 Å / Rmerge(I) obs: 4.303 / CC1/2: 0.427 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ILR Resolution: 1.8→31.833 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.44 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→31.833 Å
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Refine LS restraints |
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LS refinement shell |
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