[English] 日本語
Yorodumi- PDB-1gq9: THE STRUCTURE OF CMP:2-KETO-3-DEOXY-MANNO-OCTONIC ACID SYNTHETASE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gq9 | ||||||
---|---|---|---|---|---|---|---|
Title | THE STRUCTURE OF CMP:2-KETO-3-DEOXY-MANNO-OCTONIC ACID SYNTHETASE COMPLEXED WITH CTP at 100K | ||||||
Components | 3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / NUCLEOTIDYLTRANSFERASE / CMP-KDO SYNTHETASE / NUCLEOSIDE MONOPHOSPHATE GLYCOSIDES / LIPOPOLYSACCHARIDE BIOSYNTHESIS / SUGAR-ACTIVATING ENZYMES | ||||||
Function / homology | Function and homology information 3-deoxy-manno-octulosonate cytidylyltransferase / 3-deoxy-manno-octulosonate cytidylyltransferase activity / CMP-keto-3-deoxy-D-manno-octulosonic acid biosynthetic process / lipopolysaccharide biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 2.6 Å | ||||||
Authors | Jelakovic, S. / Schulz, G.E. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Catalytic Mechanism of Cmp:2-Keto-3-Deoxy-Manno-Octonic Acid Synthetase as Derived from Complexes with Reaction Educt and Product. Authors: Jelakovic, S. / Schulz, G.E. #1: Journal: J.Mol.Biol. / Year: 2001 Title: The Structure of Cmp:2-Keto-3-Deoxy-Manno-Octonic Acid Synthetase and of its Complexes with Substrates and Substrate Analogs Authors: Jelakovic, S. / Schulz, G.E. #2: Journal: FEBS Lett. / Year: 1996 Title: The Three-Dimensional Structure of Capsule-Specific Cmp:2-Keto-3-Deoxy-Manno-Octonic Acid Synthetase from Escherichia Coli Authors: Jelakovic, S. / Jann, K. / Schulz, G.E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1gq9.cif.gz | 99.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1gq9.ent.gz | 80.7 KB | Display | PDB format |
PDBx/mmJSON format | 1gq9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/1gq9 ftp://data.pdbj.org/pub/pdb/validation_reports/gq/1gq9 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.038442, 0.865847, -0.498829), Vector: |
-Components
#1: Protein | Mass: 27059.912 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K5 / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P42216, 3-deoxy-manno-octulosonate cytidylyltransferase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.93 % | ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 9.4 / Details: pH 9.40 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / Details: Jelakovic, S., (2001) J.Mol.Biol., 312, 143. | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→29 Å / Num. obs: 14812 / % possible obs: 87 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 9.9 |
Reflection | *PLUS Lowest resolution: 29 Å / % possible obs: 87 % |
Reflection shell | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 2.74 Å / % possible obs: 74 % / Redundancy: 1.6 % / Num. unique obs: 1826 / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 5.7 |
-Processing
Software | Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: OTHER / Resolution: 2.6→29 Å / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→29 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |