+Open data
-Basic information
Entry | Database: PDB / ID: 4z1d | ||||||
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Title | Structure of PEP and zinc bound KDO8PS from H.pylori | ||||||
Components | 2-dehydro-3-deoxyphosphooctonate aldolase | ||||||
Keywords | TRANSFERASE / Helicobacter pylori / lipopolysaccharide biosynthesis / ligand bound | ||||||
Function / homology | Function and homology information 3-deoxy-8-phosphooctulonate synthase / 3-deoxy-8-phosphooctulonate synthase activity / keto-3-deoxy-D-manno-octulosonic acid biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.65 Å | ||||||
Authors | Lee, B.J. / Cho, S. / Im, H. / Yoon, H.J. | ||||||
Citation | Journal: Eur.J.Med.Chem. / Year: 2016 Title: Identification of novel scaffolds for potential anti-Helicobacter pylori agents based on the crystal structure of H. pylori 3-deoxy-d-manno-octulosonate 8-phosphate synthase (HpKDO8PS). Authors: Cho, S. / Im, H. / Lee, K.Y. / Chen, J. / Kang, H.J. / Yoon, H.J. / Min, K.H. / Lee, K.R. / Park, H.J. / Lee, B.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4z1d.cif.gz | 125.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z1d.ent.gz | 95.8 KB | Display | PDB format |
PDBx/mmJSON format | 4z1d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z1/4z1d ftp://data.pdbj.org/pub/pdb/validation_reports/z1/4z1d | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 30381.914 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria) Strain: ATCC 700392 / 26695 / Gene: kdsA, HP_0003 / Plasmid: pCOLD I / Production host: Escherichia coli (E. coli) References: UniProt: P56060, 3-deoxy-8-phosphooctulonate synthase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, HEPES, magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: May 20, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. obs: 65566 / % possible obs: 99.2 % / Redundancy: 4 % / Net I/σ(I): 34.31 |
-Processing
Software |
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Refinement | Resolution: 1.65→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.9 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.131 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→50 Å
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Refine LS restraints |
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