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Yorodumi- PDB-1h7h: The structure of CMP:2-keto-3-deoxy-manno-octonic acid synthetase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h7h | ||||||
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Title | The structure of CMP:2-keto-3-deoxy-manno-octonic acid synthetase and of its complexes with substrates and substrate analogues, CDP complex | ||||||
Components | 3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE | ||||||
Keywords | 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 / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 2.3 Å | ||||||
Authors | Jelakovic, S. / Schulz, G.E. | ||||||
Citation | 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. #1: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h7h.cif.gz | 112.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h7h.ent.gz | 86.9 KB | Display | PDB format |
PDBx/mmJSON format | 1h7h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1h7h_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 1h7h_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1h7h_validation.xml.gz | 23.4 KB | Display | |
Data in CIF | 1h7h_validation.cif.gz | 33.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h7/1h7h ftp://data.pdbj.org/pub/pdb/validation_reports/h7/1h7h | HTTPS FTP |
-Related structure data
-Links
-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: (-0.050158, 0.857306, -0.512358), 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 / Gene: KPSU / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P42216, 3-deoxy-manno-octulosonate cytidylyltransferase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.44 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 9.4 / Details: pH 9.40 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 297 K |
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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: 2.3→24.8 Å / Num. obs: 24318 / % possible obs: 96 % / Redundancy: 3.2 % / Rsym value: 0.056 |
Reflection | *PLUS % possible obs: 96 % / Rmerge(I) obs: 0.056 |
Reflection shell | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 2.38 Å / % possible obs: 85 % / Redundancy: 1.7 % / Num. unique obs: 2107 / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 4.8 |
-Processing
Software | Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER / Resolution: 2.3→24.8 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE 4 C-TERMINAL RESIDUES OF SUBUNIT B WERE NOT REFINED
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Refinement step | Cycle: LAST / Resolution: 2.3→24.8 Å
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Refine LS restraints |
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Software | *PLUS Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.15 / Rfactor Rwork: 0.15 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |