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- PDB-1gqc: THE STRUCTURE OF CMP:2-KETO-3-DEOXY-MANNO-OCTONIC ACID SYNTHETASE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1gqc | ||||||
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Title | THE STRUCTURE OF CMP:2-KETO-3-DEOXY-MANNO-OCTONIC ACID SYNTHETASE COMPLEXED WITH CMP-Kdo at 100K | ||||||
![]() | 3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE | ||||||
![]() | TRANSFERASE / NUCLEOTIDYLTRANSFERASE / CMP-KDO SYNTHETASE / NUCLEOSIDE MONOPHOSPHATE GLYCOSIDES / LIPOPOLYSACCHARIDE BIOSYNTHESIS / SUGAR-ACTIVATING ENZYMES | ||||||
Function / homology | ![]() 3-deoxy-manno-octulosonate cytidylyltransferase / 3-deoxy-manno-octulosonate cytidylyltransferase activity / CMP-keto-3-deoxy-D-manno-octulosonic acid biosynthetic process / lipopolysaccharide biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Jelakovic, S. / Schulz, G.E. | ||||||
![]() | ![]() 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: ![]() 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: ![]() 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 |
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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 | ![]() | 112.3 KB | Display | ![]() |
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PDB format | ![]() | 86.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 23.5 KB | Display | |
Data in CIF | ![]() | 33.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.081444, 0.885712, -0.457036), Vector: |
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Components
#1: Protein | Mass: 27059.912 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P42216, 3-deoxy-manno-octulosonate cytidylyltransferase #2: Chemical | #3: Chemical | ChemComp-CMK / | #4: Chemical | ChemComp-C5P / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 52.97 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
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→33 Å / Num. obs: 15622 / % possible obs: 88 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 6 |
Reflection | *PLUS Lowest resolution: 33 Å / % possible obs: 88 % |
Reflection shell | *PLUS Highest resolution: 2.57 Å / Lowest resolution: 2.7 Å / % possible obs: 81 % / Redundancy: 5.7 % / Num. unique obs: 2075 / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.3 |
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Processing
Software | Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER / Resolution: 2.6→24.44 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.6→24.44 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 25 Å / Rfactor Rfree: 0.24 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |