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Yorodumi- PDB-2w1k: Crystal Structure of Sortase C-3 (SRTC-3) from Streptococcus pneu... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 2w1k | ||||||
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| Title | Crystal Structure of Sortase C-3 (SRTC-3) from Streptococcus pneumoniae | ||||||
Components | PUTATIVE SORTASE | ||||||
Keywords | TRANSFERASE / PILUS / SORTASE / PNEUMOCOCCUS / PATHOGENICITY | ||||||
| Function / homology | Function and homology information | ||||||
| Biological species | ![]() | ||||||
| Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.14 Å | ||||||
Authors | Manzano, C. / Contreras-Martel, C. / El Mortaji, L. / Izore, T. / Fenel, D. / Vernet, T. / Schoehn, G. / Di Guilmi, A.M. / Dessen, A. | ||||||
Citation | Journal: Structure / Year: 2008Title: Sortase-Mediated Pilus Fiber Biogenesis in Streptococcus Pneumoniae. Authors: Manzano, C. / Contreras-Martel, C. / El Mortaji, L. / Izore, T. / Fenel, D. / Vernet, T. / Schoehn, G. / Di Guilmi, A.M. / Dessen, A. | ||||||
| History |
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| Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA", "BA" IN EACH CHAIN ON SHEET RECORDS ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA", "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 2w1k.cif.gz | 112.9 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb2w1k.ent.gz | 89.1 KB | Display | PDB format |
| PDBx/mmJSON format | 2w1k.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 2w1k_validation.pdf.gz | 450.5 KB | Display | wwPDB validaton report |
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| Full document | 2w1k_full_validation.pdf.gz | 460.5 KB | Display | |
| Data in XML | 2w1k_validation.xml.gz | 24.8 KB | Display | |
| Data in CIF | 2w1k_validation.cif.gz | 36.8 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w1/2w1k ftp://data.pdbj.org/pub/pdb/validation_reports/w1/2w1k | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 2w1jSC S: Starting model for refinement C: citing same article ( |
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| Similar structure data |
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Links
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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: 28412.365 Da / Num. of mol.: 2 / Fragment: RESIDUES 32-283 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: Q97SB7, UniProt: A7KT36*PLUS, EC: 2.3.2.12 #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | SIGNAL PEPTIDE AND TRANSMEMBR | |
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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: 2.41 Å3/Da / Density % sol: 48.96 % / Description: NONE |
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| Crystal grow | pH: 5 / Details: 100 MM MES PH 5.0, 0.5 M (NH4)2SO4, 1.0 M LISO4 |
-Data collection
| Diffraction | Mean temperature: 100 K |
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| Diffraction source | Source: ROTATING ANODE / Type: RIGAKU ROTAFLEX / Wavelength: 1.5418 |
| Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Mar 31, 2008 |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
| Reflection | Resolution: 2.14→43.35 Å / Num. obs: 31007 / % possible obs: 90.8 % / Observed criterion σ(I): 3 / Redundancy: 6.6 % / Biso Wilson estimate: 35.09 Å2 / Rsym value: 0.1 / Net I/σ(I): 14.3 |
| Reflection shell | Resolution: 2.14→2.27 Å / Redundancy: 6 % / Mean I/σ(I) obs: 4.2 / Rsym value: 0.52 / % possible all: 76.3 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: PDB ENTRY 2W1J Resolution: 2.14→43.35 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.917 / SU B: 9.811 / SU ML: 0.139 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 37.68 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement step | Cycle: LAST / Resolution: 2.14→43.35 Å
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