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Yorodumi- PDB-4hgp: Crystal Structure of 2-keto-3-deoxyoctulosonate 8-phosphate phosp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hgp | ||||||
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Title | Crystal Structure of 2-keto-3-deoxyoctulosonate 8-phosphate phosphohydrolase from Haemophilus influenzae in complex with transition state mimic | ||||||
Components | 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC | ||||||
Keywords | HYDROLASE / Rossmann Fold / Phosphohydroylase | ||||||
Function / homology | Function and homology information 3-deoxy-manno-octulosonate-8-phosphatase / 3-deoxy-manno-octulosonate-8-phosphatase activity / lipopolysaccharide biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Haemophilus influenzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Daughtry, K.D. / Allen, K.N. | ||||||
Citation | Journal: Biochemistry / Year: 2013 Title: Structural Basis for the Divergence of Substrate Specificity and Biological Function within HAD Phosphatases in Lipopolysaccharide and Sialic Acid Biosynthesis. Authors: Daughtry, K.D. / Huang, H. / Malashkevich, V. / Patskovsky, Y. / Liu, W. / Ramagopal, U. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / Dunaway-Mariano, D. / Allen, K.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hgp.cif.gz | 53.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hgp.ent.gz | 37 KB | Display | PDB format |
PDBx/mmJSON format | 4hgp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hg/4hgp ftp://data.pdbj.org/pub/pdb/validation_reports/hg/4hgp | HTTPS FTP |
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-Related structure data
Related structure data | 3mmzC 3mn1C 3n07C 4hgnC 4hgoC 4hgqC 4hgrC 1k1eS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 19455.283 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: KW20 / Gene: HI_1679 / Plasmid: PDEST17-HI1679 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P45314, 3-deoxy-manno-octulosonate-8-phosphatase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-VN4 / |
#4: Sugar | ChemComp-KDO / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.42 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100 mM Tris, 30% polyethylene glycol 3350. Crystal soaked with 20 mM NaVN4, 20 mM KDO for 3 days. Crystal dragged through Paratone prior to flash cooling, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Jan 14, 2010 / Details: Helios multi-layer optics |
Radiation | Monochromator: rotating-anode / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→29.5 Å / Num. obs: 14655 / % possible obs: 95.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.9 % / Rsym value: 0.0573 / Net I/σ(I): 13.68 |
Reflection shell | Resolution: 1.8→1.89 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.3813 / % possible all: 91.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1k1e Resolution: 1.8→29.463 Å / σ(F): 1.38 / Phase error: 27.98 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.75 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→29.463 Å
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Refine LS restraints |
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LS refinement shell |
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