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- PDB-1rk2: E. COLI RIBOKINASE COMPLEXED WITH RIBOSE AND ADP, SOLVED IN SPACE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1rk2 | |||||||||
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Title | E. COLI RIBOKINASE COMPLEXED WITH RIBOSE AND ADP, SOLVED IN SPACE GROUP P212121 | |||||||||
![]() | RIBOKINASE | |||||||||
![]() | TRANSFERASE / CARBOHYDRATE KINASE / RIBOSE / INDUCED FIT / DOMAIN RE-ARRANGEMENTS | |||||||||
Function / homology | ![]() ribokinase / ribokinase activity / D-ribose catabolic process / protein homodimerization activity / ATP binding / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Sigrell, J.A. / Cameron, A.D. / Mowbray, S.L. | |||||||||
![]() | ![]() Title: Induced fit on sugar binding activates ribokinase. Authors: Sigrell, J.A. / Cameron, A.D. / Mowbray, S.L. #1: ![]() Title: Structure of Escherichia coli Ribokinase in Complex with Ribose and Nucleotide Determined to 1.8 A Resolution: Insights Into a New Family of Kinase Structures Authors: Sigrell, J.A. / Cameron, A.D. / Jones, T.A. / Mowbray, S.L. #2: ![]() Title: Purification, Characterization, and Crystallization of Escherichia coli Ribokinase Authors: Sigrell, J.A. / Cameron, A.D. / Jones, T.A. / Mowbray, S.L. #3: ![]() Title: Ribokinase from Escherichia coli K12. Nucleotide Sequence and Overexpression of the RBSK Gene and Purification of Ribokinase Authors: Hope, J.N. / Bell, A.W. / Hermodson, M.A. / Groarke, J.M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 245.7 KB | Display | ![]() |
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PDB format | ![]() | 195.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 49.9 KB | Display | |
Data in CIF | ![]() | 68.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1rkaC ![]() 1rksC ![]() 1rkdS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper:
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Components
-Protein / Sugars , 2 types, 8 molecules ABCD![](data/chem/img/RIB.gif)
![](data/chem/img/RIB.gif)
#1: Protein | Mass: 32320.393 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Description: THE RBSK GENE WAS CLONED BEHIND AURCE 11 TRP-PROMOTER, FORMING THE PLASMID PJGK10 Cellular location: CYTOPLASM / Gene: RBSK / Plasmid: PJGK10 / Production host: ![]() ![]() #2: Sugar | ChemComp-RIB / |
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-Non-polymers , 4 types, 421 molecules ![](data/chem/img/ALF.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ALF / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-ADP / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 33.2 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.8 Details: CRYSTALS WERE GROWN IN THE PRESENCE OF 5 MM RIBOSE, 10 MM ADP, 0.05 MM ALF4 AND 15 MM NAF USING 8.8-15% PEG 4000, 0.25 M MGCL2 AND 20% MPD IN 0.1 M TRIS- HCL BUFFERED TO PH 4.8. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1998 / Details: BENT MIRROR |
Radiation | Monochromator: TRIANGULAR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9058 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→13 Å / Num. obs: 55979 / % possible obs: 99.1 % / Redundancy: 4 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.25→2.29 Å / Redundancy: 4 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 3.9 / % possible all: 98.8 |
Reflection | *PLUS Num. measured all: 188129 |
Reflection shell | *PLUS % possible obs: 98.8 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1RKD: RESIDUES 4-9, 44-93, 123-241 AND 254-309 Resolution: 2.25→13 Å / Rfactor Rfree error: 0.005 / Data cutoff high rms absF: 2972122.44 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: TARGET WAS MLF USING AMPLITUDES. THE MAIN-CHAIN OF RESIDUES 5-13, 43-93, 116- 198, 205-235, 240-243, 247-305 AND ALF 315 WERE RESTRAINED WITH A WEIGHT OF 100.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 61.98 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→13 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.25→2.39 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.225 |