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Yorodumi- PDB-2wts: Crystal structure of sortase C-1 (SrtC-1) mutant H131D from S. pn... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wts | ||||||
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Title | Crystal structure of sortase C-1 (SrtC-1) mutant H131D from S. pneumoniae | ||||||
Components | PUTATIVE SORTASE | ||||||
Keywords | TRANSFERASE / PILI / PATHOGENICITY | ||||||
Function / homology | Function and homology information | ||||||
Biological species | STREPTOCOCCUS PNEUMONIAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Manzano, C. / Izore, T. / Job, V. / DiGuilmi, A.M. / Dessen, A. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Sortase Activity is Controlled by a Flexible Lid in the Pilus Biogenesis Mechanism of Gram-Positive Pathogens. Authors: Manzano, C. / Izore, T. / Job, V. / Di Guilmi, A.M. / Dessen, A. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wts.cif.gz | 199.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wts.ent.gz | 160 KB | Display | PDB format |
PDBx/mmJSON format | 2wts.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wts_validation.pdf.gz | 459.8 KB | Display | wwPDB validaton report |
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Full document | 2wts_full_validation.pdf.gz | 464.5 KB | Display | |
Data in XML | 2wts_validation.xml.gz | 25 KB | Display | |
Data in CIF | 2wts_validation.cif.gz | 38.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wt/2wts ftp://data.pdbj.org/pub/pdb/validation_reports/wt/2wts | HTTPS FTP |
-Related structure data
Related structure data | 2w1jS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 23789.891 Da / Num. of mol.: 2 / Fragment: RESIDUES 17-228 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: TIGR4 / Plasmid: PLIM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): RIL References: UniProt: Q97SB9, UniProt: A0A0H2UNQ9*PLUS, EC: 2.3.2.12 #2: Chemical | #3: Chemical | ChemComp-ALA / | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.5 % / Description: NONE |
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Crystal grow | Temperature: 293 K Details: 100 MM TRIS-HCL PH 8.5, 200 MM MGCL2 HEXAHYDRATE, 30% W/V POLYETHYLENE GLYCOL 4000 AT 20C. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98088 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 22, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98088 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→50 Å / Num. obs: 99255 / % possible obs: 95.3 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.3→3.89 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.19 / % possible all: 88.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2W1J Resolution: 1.3→19.81 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.744 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.052 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.989 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→19.81 Å
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Refine LS restraints |
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