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Open data
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Basic information
Entry | Database: PDB / ID: 2pjj | ||||||
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Title | E. coli lytic transglycosylase MltA-D308A in apo-1 form | ||||||
![]() | Membrane-bound lytic murein transglycosylase A | ||||||
![]() | HYDROLASE / double-psi beta-barrel / protein-sugar complex / lytic transglycosylase | ||||||
Function / homology | ![]() : / lytic transglycosylase activity / peptidoglycan turnover / hydrolase activity, hydrolyzing O-glycosyl compounds / peptidoglycan catabolic process / cell outer membrane / cell wall organization / outer membrane-bounded periplasmic space Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | van Straaten, K.E. / Dijkstra, B.W. / Thunnissen, A.M.W.H. | ||||||
![]() | ![]() Title: Structure of Escherichia coli Lytic transglycosylase MltA with bound chitohexaose: implications for peptidoglycan binding and cleavage Authors: van Straaten, K.E. / Barends, T.R. / Dijkstra, B.W. / Thunnissen, A.M.W.H. #1: ![]() Title: Escherichia coli MltA: MAD phasing and refinement of a tetartohedrally twinned protein crystal structure Authors: Barends, T.R.M. / de Jong, R.M. / van Straaten, K.E. / Thunnissen, A.M.W.H. / Dijkstra, B.W. #2: ![]() Title: Crystal structure of MltA from Escherichia coli reveals a unique lytic transglycosylase fold Authors: van Straaten, K.E. / Dijkstra, B.W. / Vollmer, W. / Thunnissen, A.M.W.H. #3: ![]() Title: Purification, crystallization and preliminary X-ray analysis of the lytic transglycosylase MltA from Escherichia coli Authors: van Straaten, K.E. / Dijkstra, B.W. / Thunnissen, A.M.W.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84.2 KB | Display | ![]() |
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PDB format | ![]() | 61.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426.8 KB | Display | ![]() |
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Full document | ![]() | 430.4 KB | Display | |
Data in XML | ![]() | 16.3 KB | Display | |
Data in CIF | ![]() | 23.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2pi8C ![]() 2picC ![]() 2ae0S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 38206.680 Da / Num. of mol.: 1 / Mutation: D308A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0A935, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.57 Å3/Da / Density % sol: 73.06 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 0.25-0.35M NaCl, 10mM magnesium chloride, 100mM sodium acetate buffer, pH 4.2, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.46→30 Å / Num. all: 25918 / Num. obs: 25840 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Biso Wilson estimate: 46.3 Å2 / Rmerge(I) obs: 0.06 / Χ2: 1.085 / Net I/σ(I): 20.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 2AE0 Resolution: 2.46→14.94 Å / Rfactor Rfree error: 0.006 / FOM work R set: 0.849 / Data cutoff high absF: 1353221.875 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.755 Å2 / ksol: 0.355 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2.46→14.94 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26
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Xplor file |
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