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Yorodumi- PDB-3f5f: Crystal structure of heparan sulfate 2-O-sulfotransferase from ga... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f5f | |||||||||
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Title | Crystal structure of heparan sulfate 2-O-sulfotransferase from gallus gallus as a maltose binding protein fusion. | |||||||||
Components | Maltose-binding periplasmic protein, Heparan sulfate 2-O-sulfotransferase 1 | |||||||||
Keywords | Transport / Transferase / maltose binding protein / fusion / heparan sulfate biosynthesis / sulfotransferase / Glycoprotein / Golgi apparatus / Membrane / Signal-anchor / Transmembrane / Periplasm / Sugar transport | |||||||||
Function / homology | Function and homology information heparan sulfate 2-O-sulfotransferase activity / HS-GAG biosynthesis / Transferases; Transferring sulfur-containing groups; Sulfotransferases / ureteric bud formation / heparan sulfate proteoglycan biosynthetic process, enzymatic modification / heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process / heparin metabolic process / detection of maltose stimulus / maltose transport complex / carbohydrate transport ...heparan sulfate 2-O-sulfotransferase activity / HS-GAG biosynthesis / Transferases; Transferring sulfur-containing groups; Sulfotransferases / ureteric bud formation / heparan sulfate proteoglycan biosynthetic process, enzymatic modification / heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process / heparin metabolic process / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / gene expression / periplasmic space / Golgi membrane / DNA damage response / identical protein binding / membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) Gallus gallus (chicken) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | |||||||||
Authors | Bethea, H.N. / Xu, D. / Liu, J. / Pedersen, L.C. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2008 Title: Redirecting the substrate specificity of heparan sulfate 2-O-sulfotransferase by structurally guided mutagenesis. Authors: Bethea, H.N. / Xu, D. / Liu, J. / Pedersen, L.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3f5f.cif.gz | 150.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f5f.ent.gz | 114 KB | Display | PDB format |
PDBx/mmJSON format | 3f5f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3f5f_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 3f5f_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3f5f_validation.xml.gz | 27.1 KB | Display | |
Data in CIF | 3f5f_validation.cif.gz | 38 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/3f5f ftp://data.pdbj.org/pub/pdb/validation_reports/f5/3f5f | HTTPS FTP |
-Related structure data
Related structure data | 3dm0S S: Starting model for refinement |
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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
#1: Protein | Mass: 74286.336 Da / Num. of mol.: 1 / Fragment: P0AEX9 residues 27-392, Q76KB1 residues 69-356 / Mutation: E359A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria), (gene. exp.) Gallus gallus (chicken) Gene: b4034, HS2ST, HS2ST1, JW3994, malE, HS2ST, HS2ST1, malE Plasmid: modified pMAL-c2x / Production host: Escherichia coli (E. coli) / Strain (production host): OrigamiB(DE3) References: UniProt: P0AEX9, UniProt: Q76KB1, Transferases; Transferring sulfur-containing groups; Sulfotransferases |
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#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
#3: Chemical | ChemComp-A3P / |
#4: 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: 3.88 Å3/Da / Density % sol: 68.29 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Ammonium Citrate, Bis-tris-propane, Phenol, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 92 / Detector: CCD / Date: Oct 1, 2008 / Details: Varimax HF |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→50 Å / Num. all: 33196 / Num. obs: 33063 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 38.8 Å2 / Rsym value: 0.086 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.65→2.74 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 3261 / Rsym value: 0.541 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3DM0 Resolution: 2.65→28.85 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 625197.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 27.9365 Å2 / ksol: 0.311599 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.65→28.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.82 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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