+Open data
-Basic information
Entry | Database: PDB / ID: 1qxa | ||||||
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Title | Crystal structure of Sortase B complexed with Gly3 | ||||||
Components |
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Keywords | HYDROLASE / Sortase / transpeptidase / cysteine protease | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Zong, Y. / Mazmanian, S.K. / Schneewind, O. / Narayana, S.V. | ||||||
Citation | Journal: Structure / Year: 2004 Title: The structure of sortase B, a cysteine transpeptidase that tethers surface protein to the Staphylococcus aureus cell wall Authors: Zong, Y. / Mazmanian, S.K. / Schneewind, O. / Narayana, S.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qxa.cif.gz | 54.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qxa.ent.gz | 42.1 KB | Display | PDB format |
PDBx/mmJSON format | 1qxa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/1qxa ftp://data.pdbj.org/pub/pdb/validation_reports/qx/1qxa | HTTPS FTP |
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-Related 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: 27920.346 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NX63, UniProt: Q2FZE3*PLUS |
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#2: Protein/peptide | Mass: 189.171 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Chemical | ChemComp-ETM / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: Ammonium Sulfate, Sodium Chloride, MES, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 19, 2002 |
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: 2.5→50 Å / Num. all: 7109 / Num. obs: 6905 / % possible obs: 96.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.11 |
Reflection shell | Resolution: 2.5→2.6 Å / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→33.3 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 237868.26 / Data cutoff high rms absF: 237868.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.2203 Å2 / ksol: 0.395327 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→33.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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