+Open data
-Basic information
Entry | Database: PDB / ID: 1rkd | |||||||||
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Title | E. COLI RIBOKINASE COMPLEXED WITH RIBOSE AND ADP | |||||||||
Components | RIBOKINASE | |||||||||
Keywords | CARBOHYDRATE KINASE / RIBOSE / NUCLEOTIDE BINDING / TRANSFERASE | |||||||||
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 / MIR / Resolution: 1.84 Å | |||||||||
Authors | Sigrell, J.A. / Cameron, A.D. / Jones, T.A. / Mowbray, S.L. | |||||||||
Citation | Journal: Structure / Year: 1998 Title: Structure of Escherichia coli ribokinase in complex with ribose and dinucleotide 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. #1: 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. #2: 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 | 1rkd.cif.gz | 74.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rkd.ent.gz | 55.7 KB | Display | PDB format |
PDBx/mmJSON format | 1rkd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rkd_validation.pdf.gz | 816 KB | Display | wwPDB validaton report |
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Full document | 1rkd_full_validation.pdf.gz | 816.3 KB | Display | |
Data in XML | 1rkd_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 1rkd_validation.cif.gz | 22.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rk/1rkd ftp://data.pdbj.org/pub/pdb/validation_reports/rk/1rkd | HTTPS FTP |
-Related structure data
Similar structure data |
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-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: 32320.393 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 Description: THE RBSK GENE WAS CLONED BEHIND A TRP-PROMOTER, FORMING THE PLASMID PJGK10 Cell line: S2 / Cellular location: CYTOPLASM / Gene: RBSK / Plasmid: PJGK10 / Production host: Escherichia coli (E. coli) / Strain (production host): MRI240 / References: UniProt: P0A9J6, ribokinase | ||||
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#2: Sugar | ChemComp-RIB / | ||||
#3: Chemical | #4: Chemical | ChemComp-ADP / | #5: 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: 3.1 Å3/Da / Density % sol: 49 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.4 Details: CRYSTALS WERE GROWN IN THE PRESENCE OF 0.5 MM RIBOSE, 10 MM AMP-PNP AND 10 MM MGCL2 USING 2.1-2.4 M NH4H2PO4 AS PRECIPITANT AND BUFFERED TO PH 8.4 WITH 0.1 M TRIS-HCL. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Sigrell, J.A., (1997) Protein Sci., 6, 2474. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8893 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8893 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→30 Å / Num. obs: 35015 / % possible obs: 95.5 % / Redundancy: 7.5 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 30.2 |
Reflection shell | Resolution: 1.84→1.87 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 7.4 / % possible all: 97.8 |
Reflection | *PLUS Num. measured all: 279852 |
Reflection shell | *PLUS % possible obs: 97.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.84→28 Å / Cross valid method: THROUGHOUT Details: THE BULK SOLVENT CORRECTION WAS CALCULATED IN X-PLOR. AMP-PNP WAS INCLUDED IN THE CRYSTALLIZATION MIXTURE, BUT THE GAMMA-PHOSPHATE COULD NOT BE DETECTED. THE AUTHORS THEREFORE TREAT ...Details: THE BULK SOLVENT CORRECTION WAS CALCULATED IN X-PLOR. AMP-PNP WAS INCLUDED IN THE CRYSTALLIZATION MIXTURE, BUT THE GAMMA-PHOSPHATE COULD NOT BE DETECTED. THE AUTHORS THEREFORE TREAT HYDROLYSED ATP-ANALOGUE AS ADP IN THE MODEL.
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Displacement parameters | Biso mean: 29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati sigma a obs: 0.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.84→28 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.22 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |