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Yorodumi- PDB-5za4: Crystal structure of Sialic acid Binding protein from Haemophilus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5za4 | |||||||||
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Title | Crystal structure of Sialic acid Binding protein from Haemophilus ducreyi | |||||||||
Components | Putative ABC transporter periplasmic binding protein | |||||||||
Keywords | SUGAR BINDING PROTEIN / three domain proteins / sialic acid Neu5Gc / molecular mimicry / adhesion / cell signaling / nutrition | |||||||||
Function / homology | Function and homology information peptide transmembrane transporter activity / peptide transport / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space Similarity search - Function | |||||||||
Biological species | Haemophilus ducreyi (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.193 Å | |||||||||
Authors | Setty, T.G. / Subramanian, R. | |||||||||
Funding support | India, 2items
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Citation | Journal: J. Biol. Chem. / Year: 2018 Title: Molecular characterization of the interaction of sialic acid with the periplasmic binding protein fromHaemophilus ducreyi. Authors: Gangi Setty, T. / Mowers, J.C. / Hobbs, A.G. / Maiya, S.P. / Syed, S. / Munson Jr., R.S. / Apicella, M.A. / Subramanian, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5za4.cif.gz | 110.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5za4.ent.gz | 83.1 KB | Display | PDB format |
PDBx/mmJSON format | 5za4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5za4_validation.pdf.gz | 424.1 KB | Display | wwPDB validaton report |
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Full document | 5za4_full_validation.pdf.gz | 432.1 KB | Display | |
Data in XML | 5za4_validation.xml.gz | 20.2 KB | Display | |
Data in CIF | 5za4_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/za/5za4 ftp://data.pdbj.org/pub/pdb/validation_reports/za/5za4 | HTTPS FTP |
-Related structure data
Related structure data | 5yybC 5z99SC 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
#1: Protein | Mass: 54390.746 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus ducreyi (bacteria) / Strain: 35000HP / ATCC 700724 / Gene: HD_1669 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7VL18 |
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#2: 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: 2.19 Å3/Da / Density % sol: 43.84 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.2M Sodium Iodide 20% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.0396 Å | ||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Nov 20, 2006 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0396 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.19→29.43 Å / Num. obs: 24030 / % possible obs: 99.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 24.38 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.178 / Rpim(I) all: 0.108 / Rrim(I) all: 0.209 / Net I/σ(I): 7 / Num. measured all: 90314 / Scaling rejects: 30 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5Z99 Resolution: 2.193→29.429 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 28.02 / Stereochemistry target values: ML
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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 max: 81.81 Å2 / Biso mean: 28.9139 Å2 / Biso min: 9.89 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.193→29.429 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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