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Yorodumi- PDB-2mlm: Solution structure of sortase A from S. aureus in complex with be... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2mlm | ||||||
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Title | Solution structure of sortase A from S. aureus in complex with benzo[d]isothiazol-3-one based inhibitor | ||||||
Components | Sortase family protein | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Sortase; Chain: A; / Sortase / Beta Barrel / Mainly Beta / Chem-2W7 / : Function and homology information | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | SOLUTION NMR / torsion angle dynamics, simulated annealing | ||||||
Model details | closest to the average, model1 | ||||||
Authors | Jaudzems, K. / Zhulenkovs, D. / Leonchiks, A. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2014 Title: Discovery and structure-activity relationship studies of irreversible benzisothiazolinone-based inhibitors against Staphylococcus aureus sortase A transpeptidase. Authors: Zhulenkovs, D. / Rudevica, Z. / Jaudzems, K. / Turks, M. / Leonchiks, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2mlm.cif.gz | 931.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2mlm.ent.gz | 811.5 KB | Display | PDB format |
PDBx/mmJSON format | 2mlm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2mlm_validation.pdf.gz | 497.6 KB | Display | wwPDB validaton report |
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Full document | 2mlm_full_validation.pdf.gz | 645.3 KB | Display | |
Data in XML | 2mlm_validation.xml.gz | 68.7 KB | Display | |
Data in CIF | 2mlm_validation.cif.gz | 83.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/2mlm ftp://data.pdbj.org/pub/pdb/validation_reports/ml/2mlm | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 16825.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: CA347_2602 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: R9YTM5 |
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#2: Chemical | ChemComp-2W7 / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.6 mM [U-100% 13C; U-100% 15N] sortase A-1, 2.4 mM N-(adamantan-1-yl)-2-(3-oxo-2,3-dihydro-1,2-benzothiazol-2-yl)-acetamide-2, 5.0 % [U-100% 2H] D2O-3, 2.4 % [U-100% 2H] DMSO-4, 20 mM [U- ...Contents: 1.6 mM [U-100% 13C; U-100% 15N] sortase A-1, 2.4 mM N-(adamantan-1-yl)-2-(3-oxo-2,3-dihydro-1,2-benzothiazol-2-yl)-acetamide-2, 5.0 % [U-100% 2H] D2O-3, 2.4 % [U-100% 2H] DMSO-4, 20 mM [U-100% 2H] sodium acetate-5, 50 mM sodium chloride-6, 10 mM calcium chloride-7, 95% H2O/5% D2O Solvent system: 95% H2O/5% D2O | ||||||||||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.1 / pH: 6 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics, simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 1670 / NOE intraresidue total count: 570 / NOE long range total count: 482 / NOE medium range total count: 156 / NOE sequential total count: 462 | ||||||||||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 | ||||||||||||||||||||||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.0156 Å / Distance rms dev error: 0.0013 Å |