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Open data
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Basic information
Entry | Database: PDB / ID: 1gqt | ||||||||||||
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Title | Activation of Ribokinase by Monovalent Cations | ||||||||||||
![]() | RIBOKINASE | ||||||||||||
![]() | TRANSFERASE / CARBOHYDRATE KINASE / RIBOSE / INDUCED FIT / BINDING OF MONOVALENT CATIONS / ACTIVATION BY MONOVALENT CATIONS | ||||||||||||
Function / homology | ![]() ribokinase / ribokinase activity / D-ribose catabolic process / protein homodimerization activity / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Andersson, C.E. / Mowbray, S.L. | ||||||||||||
![]() | ![]() Title: Activation of Ribokinase by Monovalent Cations. Authors: Andersson, C.E. / Mowbray, S.L. #1: ![]() 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: ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 241.4 KB | Display | ![]() |
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PDB format | ![]() | 193.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 48.2 KB | Display | |
Data in CIF | ![]() | 66.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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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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Components
#1: Protein | Mass: 32320.393 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() 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: ![]() |
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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: ![]() ![]() ![]() |
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 % |
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Processing
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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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