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Yorodumi- PDB-4ff5: Structure basis of a novel virulence factor GHIP a glycosyl hydro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ff5 | ||||||
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Title | Structure basis of a novel virulence factor GHIP a glycosyl hydrolase 25 of Streptococcus pneumoniae participating in host cell invasion | ||||||
Components | Glycosyl hydrolase 25Glycoside hydrolase | ||||||
Keywords | HYDROLASE / TIM fold / outer surface | ||||||
Function / homology | Function and homology information peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme activity / membrane => GO:0016020 Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.86 Å | ||||||
Authors | Wang, D. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Structural basis of the novel S. pneumoniae virulence factor, GHIP, a glycosyl hydrolase 25 participating in host-cell invasion. Authors: Niu, S. / Luo, M. / Tang, J. / Zhou, H. / Zhang, Y. / Min, X. / Cai, X. / Zhang, W. / Xu, W. / Li, D. / Ding, J. / Hu, Y. / Wang, D. / Huang, A. / Yin, Y. / Wang, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ff5.cif.gz | 107.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ff5.ent.gz | 82.5 KB | Display | PDB format |
PDBx/mmJSON format | 4ff5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/4ff5 ftp://data.pdbj.org/pub/pdb/validation_reports/ff/4ff5 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30089.098 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: SP_0987 / Production host: Escherichia coli (E. coli) / Strain (production host): B834, BL21 / References: UniProt: Q97R47, UniProt: A0A0H2UPQ2*PLUS | ||
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#2: Chemical | ChemComp-EDO / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.31 Details: 26% polyethylene glycol (PEG) 3350,0.2 M lithium citrate,Bis-Tris pH 7.31, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.85→50 Å / Num. all: 171963 / Num. obs: 19741 / % possible obs: 95.1 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.029 / Rsym value: 0.045 / Net I/σ(I): 14.5 | |||||||||||||||
Reflection shell | Resolution: 2.4→2.63 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.052 / Mean I/σ(I) obs: 8670 / Rsym value: 0.046 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.86→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.917 / SU B: 6.158 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 23.374 Å2
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Refinement step | Cycle: LAST / Resolution: 1.86→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.86→1.908 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 0.0418 Å / Origin y: 14.683 Å / Origin z: 17.7468 Å
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