+Open data
-Basic information
Entry | Database: PDB / ID: 1t2w | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of Sortase A in Complex with a LPETG peptide | |||||||||
Components |
| |||||||||
Keywords | HYDROLASE / Sortase / transpeptidase / BETA BARREL | |||||||||
Function / homology | Function and homology information 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 | Staphylococcus aureus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Zong, Y. / Bice, T.W. / Ton-That, H. / Schneewind, O. / Narayana, S.V. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Crystal structure of Staphylococcus aureus sortase A and its substrate complex Authors: Zong, Y. / Bice, T.W. / Ton-That, H. / Schneewind, O. / Narayana, S.V. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1t2w.cif.gz | 102.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1t2w.ent.gz | 77.8 KB | Display | PDB format |
PDBx/mmJSON format | 1t2w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t2/1t2w ftp://data.pdbj.org/pub/pdb/validation_reports/t2/1t2w | HTTPS FTP |
---|
-Related structure data
Related structure data | 1t2oSC 1t2pC C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 16390.531 Da / Num. of mol.: 3 / Fragment: Sortase A (residues 62-206) complexed with LPETG / Mutation: C184A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) Gene: srtA, srtA_2, A7Q05_0203, A7U51_2758, DD547_02559, DQV53_14585, EP54_00580, EQ90_03180, ER624_01345, ERS365775_01887, FA040_11075, G6Y10_05930, GO814_08865, GZ145_04475, H4Q63_05340, HMPREF2819_ ...Gene: srtA, srtA_2, A7Q05_0203, A7U51_2758, DD547_02559, DQV53_14585, EP54_00580, EQ90_03180, ER624_01345, ERS365775_01887, FA040_11075, G6Y10_05930, GO814_08865, GZ145_04475, H4Q63_05340, HMPREF2819_05680, HMPREF3211_00152, HT539_09110, HW113_13780, HYH24_12580, LG33_14175, NCTC10654_02700, NCTC10988_02942, RK65_002860, SABB_01155, SAHC1340_00378, SAMEA103891215_00596, SAMEA103891286_01213, SAMEA103891321_01196, SAMEA1966928_00247, SAMEA1969845_01250, SAMEA1972827_00954, SAMEA2076218_00454, SAMEA2076226_00491, SAMEA2076235_01010, SAMEA2076464_00854, SAMEA2076470_01152, SAMEA2076472_01070, SAMEA2076475_01144, SAMEA2076481_00167, SAMEA2076758_00629, SAMEA2077031_00874, SAMEA2077046_00836, SAMEA2077832_00359, SAMEA2078252_01155, SAMEA2078307_01069, SAMEA2078308_00562, SAMEA2078558_00738, SAMEA2078569_01198, SAMEA2078588_01162, SAMEA2078824_00854, SAMEA2078837_00966, SAMEA2079048_01261, SAMEA2079512_01291, SAMEA2079517_02158, SAMEA2079727_00616, SAMEA2079728_00978, SAMEA2079949_00908, SAMEA2079951_00489, SAMEA2079957_00669, SAMEA2079958_00786, SAMEA2079968_00740, SAMEA2080812_00148, SAMEA2080900_00941, SAMEA2080904_01047, SAMEA2080913_01192, SAMEA2081043_00247, SAMEA2081054_00932, SAMEA2081211_00203, SAMEA2081362_00521, SAMEA2081458_00784, SAMEA2081475_00930, SAMEA4008573_00649, SAMEA4008676_00205, SAMEA958779_01435, SAMEA958793_00205, SAMEA958804_00204, SAMEA958836_00599, SAMEA958838_01748, SAMEA958987_01810 Plasmid: Novagen pET 15b / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-blue / References: UniProt: Q9S446 #2: Protein/peptide | | Mass: 515.557 Da / Num. of mol.: 1 / Source method: obtained synthetically #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 40 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9979 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 5, 2002 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9979 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→27.31 Å / Num. all: 37608 / Num. obs: 34240 / % possible obs: 91.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 11 Å2 |
Reflection shell | Resolution: 1.8→1.9 Å / % possible all: 91.2 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1T2O Resolution: 1.8→27.31 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 766432.57 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.0958 Å2 / ksol: 0.408279 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 34 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→27.31 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
| |||||||||||||||||||||||||
Xplor file |
|