[English] 日本語
Yorodumi- PDB-2cgk: Crystal Structure of L-rhamnulose kinase from Escherichia coli in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cgk | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of L-rhamnulose kinase from Escherichia coli in an open uncomplexed conformation. | ||||||
Components | L-RHAMNULOSE KINASE | ||||||
Keywords | TRANSFERASE / L-RHAMNULOSE KINASE / RHAMNOSE DEGRADATION / HEXOKINASE-HSP70- ACTIN SUPERFAMILY / INDUCED FIT / IN-LINE PHOSPHORYL TRANSFER / KINASE / RHAMNOSE METABOLISM | ||||||
Function / homology | Function and homology information rhamnulokinase / rhamnulokinase activity / glycerol kinase activity / rhamnose catabolic process / glycerol metabolic process / phosphorylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI BL21 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å | ||||||
Authors | Grueninger, D. / Schulz, G.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Structure and Reaction Mechanism of L-Rhamnulose Kinase from Escherichia Coli. Authors: Grueninger, D. / Schulz, G.E. | ||||||
History |
| ||||||
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 |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2cgk.cif.gz | 192.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2cgk.ent.gz | 154.1 KB | Display | PDB format |
PDBx/mmJSON format | 2cgk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cg/2cgk ftp://data.pdbj.org/pub/pdb/validation_reports/cg/2cgk | HTTPS FTP |
---|
-Related structure data
Related structure data | 2cgjC 2cglSC C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.99999, 0.00391, -0.00275), Vector: |
-Components
#1: Protein | Mass: 53954.715 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI BL21(DE3) (bacteria) / Plasmid: PKK223-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM105 References: UniProt: Q8X899, UniProt: P32171*PLUS, rhamnulokinase #2: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, GLU 69 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLU 70 TO ALA ...ENGINEERED | Sequence details | THE SEQUENCE DISCREPANCIES ARE BECAUSE THE DATABASE SEQUENCE IS FROM E.COLI STRAIN O157-H7. THE ...THE SEQUENCE DISCREPANC | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 40 % |
---|---|
Crystal grow | Details: 17 % PEG 8000, 120 MM LICL |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9184 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 26, 2005 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.46→52 Å / Num. obs: 29856 / % possible obs: 95.1 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.46→2.54 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.6 / % possible all: 97.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CGL Resolution: 2.46→44 Å / Data cutoff high absF: 10000 / Cross valid method: RMSD / σ(F): 0 Stereochemistry target values: MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES Details: THE STRUCTURE WAS REFINED USING STRICT NCS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: CNS BULK SOLVENT MODEL USED / Bsol: 28.1832 Å2 / ksol: 0.340036 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.9 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.46→44 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.46→2.55 Å / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|