+Open data
-Basic information
Entry | Database: PDB / ID: 1gqt | ||||||||||||
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Title | Activation of Ribokinase by Monovalent Cations | ||||||||||||
Components | RIBOKINASE | ||||||||||||
Keywords | TRANSFERASE / CARBOHYDRATE KINASE / RIBOSE / INDUCED FIT / BINDING OF MONOVALENT CATIONS / ACTIVATION BY MONOVALENT CATIONS | ||||||||||||
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 / OTHER / Resolution: 2.34 Å | ||||||||||||
Authors | Andersson, C.E. / Mowbray, S.L. | ||||||||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Activation of Ribokinase by Monovalent Cations. Authors: Andersson, C.E. / Mowbray, S.L. #1: 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. #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. #3: Journal: J. Mol. Biol. / Year: 1999 Title: Induced fit on sugar binding activates ribokinase. Authors: Sigrell, J.A. / Cameron, A.D. / Mowbray, S.L. | ||||||||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gqt.cif.gz | 235.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gqt.ent.gz | 193.6 KB | Display | PDB format |
PDBx/mmJSON format | 1gqt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/1gqt ftp://data.pdbj.org/pub/pdb/validation_reports/gq/1gqt | HTTPS FTP |
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-Related structure data
Related structure data | |
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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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-Components
#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) / Strain: K12 / Plasmid: PJGK10 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): MRI240 References: UniProt: P05054, UniProt: P0A9J6*PLUS, ribokinase #2: Chemical | ChemComp-CS / #3: Chemical | #4: Sugar | ChemComp-RIB / #5: Water | ChemComp-HOH / | Compound details | COMPOUND | |
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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: 44.6 % Description: COORDINATES FROM 1RK2 WERE USED DIRECTLY IN REFINMENT. S.A. IN CNS WAS USED TO REMOVE MODEL BIAS. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.8 Details: CRYSTALS WERE GROWN IN DROPS CONTAINING 0.3 MM WILD-TYPE RK, 5 MM D-RIBOSE, 10 MM AMP-PCP, 75 MM MGCL2, 60 MM CSCL, 10% 2-METHYL-2,4-PENTANEDIOL, 10% POLYETHYLENE GLYCOL 4000 AND 50 MM SODIUM ACETATE, PH 4.8. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / pH: 4.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 26, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.34→17 Å / Num. obs: 50296 / % possible obs: 98.2 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.34→2.38 Å / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 3.8 / % possible all: 99.9 |
Reflection | *PLUS Num. measured all: 245133 |
Reflection shell | *PLUS % possible obs: 99.9 % |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2.34→17 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.895 / SU B: 7.927 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.428 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.34→17 Å
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