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Yorodumi- PDB-1rk2: E. COLI RIBOKINASE COMPLEXED WITH RIBOSE AND ADP, SOLVED IN SPACE... -
+Open data
-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 | |||||||||
Components | RIBOKINASE | |||||||||
Keywords | TRANSFERASE / CARBOHYDRATE KINASE / RIBOSE / INDUCED FIT / DOMAIN RE-ARRANGEMENTS | |||||||||
Function / homology | Function and homology information ribokinase / ribokinase activity / D-ribose catabolic process / protein homodimerization activity / ATP binding / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | |||||||||
Authors | Sigrell, J.A. / Cameron, A.D. / Mowbray, S.L. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Induced fit on sugar binding activates ribokinase. Authors: Sigrell, J.A. / Cameron, A.D. / Mowbray, S.L. #1: Journal: Structure / Year: 1998 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: Journal: Protein Sci. / Year: 1997 Title: Purification, Characterization, and Crystallization of Escherichia coli Ribokinase Authors: Sigrell, J.A. / Cameron, A.D. / Jones, T.A. / Mowbray, S.L. #3: Journal: J.Biol.Chem. / Year: 1986 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rk2.cif.gz | 245.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rk2.ent.gz | 195.3 KB | Display | PDB format |
PDBx/mmJSON format | 1rk2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rk/1rk2 ftp://data.pdbj.org/pub/pdb/validation_reports/rk/1rk2 | HTTPS FTP |
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-Related structure data
Related structure data | 1rkaC 1rksC 1rkdS 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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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
#1: Protein | Mass: 32320.393 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Description: THE RBSK GENE WAS CLONED BEHIND AURCE 11 TRP-PROMOTER, FORMING THE PLASMID PJGK10 Cellular location: CYTOPLASM / Gene: RBSK / Plasmid: PJGK10 / Production host: Escherichia coli (E. coli) / Strain (production host): MRI240 / References: UniProt: P0A9J6, ribokinase #2: Sugar | ChemComp-RIB / |
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-Non-polymers , 4 types, 421 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9058 |
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 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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 |