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Open data
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Basic information
Entry | Database: PDB / ID: 1t2p | ||||||
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Title | Crystal structure of Sortase A from Staphylococcus aureus | ||||||
![]() | sortase | ||||||
![]() | HYDROLASE / Sortase / BETA BARREL / transpeptidase | ||||||
Function / homology | ![]() calcium-dependent cysteine-type endopeptidase activity / ion binding / peptide binding / manganese ion binding / calcium ion binding / magnesium ion binding / proteolysis Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Zong, Y. / Bice, T.W. / Ton-That, H. / Schneewind, O. / Narayana, S.V. | ||||||
![]() | ![]() Title: CRYSTAL STRUCTURES OF STAPHYLOCOCCUS AUREUS SORTASE A AND ITS SUBSTRATE COMPLEX Authors: Zong, Y. / Bice, T.W. / Ton-That, H. / Schneewind, O. / Narayana, S.V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.3 KB | Display | ![]() |
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PDB format | ![]() | 78.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.9 KB | Display | ![]() |
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Full document | ![]() | 454.7 KB | Display | |
Data in XML | ![]() | 23.1 KB | Display | |
Data in CIF | ![]() | 33 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1t2oSC ![]() 1t2wC 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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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 16493.676 Da / Num. of mol.: 3 / Fragment: Delta-N59 (residues 61-206) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 40 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.35 Details: Ammonium Sulfate, MES, Sodium Chloride, pH 6.35, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 18, 2002 / Details: mirrors |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→1.85 Å / Num. all: 34566 / Num. obs: 33894 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 10 Å2 |
Reflection shell | Resolution: 1.75→1.85 Å / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1T2O Resolution: 2→35.52 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 385696.14 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 72.9362 Å2 / ksol: 0.37371 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→35.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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