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- PDB-1d9u: BACTERIOPHAGE LAMBDA LYSOZYME COMPLEXED WITH A CHITOHEXASACHARIDE -
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Open data
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Basic information
Entry | Database: PDB / ID: 1d9u | |||||||||
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Title | BACTERIOPHAGE LAMBDA LYSOZYME COMPLEXED WITH A CHITOHEXASACHARIDE | |||||||||
![]() | BACTERIOPHAGE LAMBDA LYSOZYME | |||||||||
![]() | HYDROLASE / GLYCOSIDASE / TRANSGLYCOSYLASE / LYSOZYME / SIX-SUGAR COMPLEX | |||||||||
Function / homology | ![]() : / lytic transglycosylase activity / viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme activity / host cell cytoplasm / defense response to bacterium Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Leung, A.K.W. / Duewel, H.S. / Honek, J.F. / Berghuis, A.M. | |||||||||
![]() | ![]() Title: Crystal structure of the lytic transglycosylase from bacteriophage lambda in complex with hexa-N-acetylchitohexaose. Authors: Leung, A.K. / Duewel, H.S. / Honek, J.F. / Berghuis, A.M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 77.7 KB | Display | ![]() |
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PDB format | ![]() | 59.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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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Unit cell |
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Components
#1: Protein | Mass: 17395.701 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.98 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: microdialysis / pH: 4.7 Details: PEG 2000 MME, Ammonium Sulfate, pH 4.7, MICRODIALYSIS, temperature 298K | ||||||||||||||||||||
Crystal grow | *PLUS pH: 4.6 | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Aug 30, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→40 Å / Num. all: 108652 / Num. obs: 14138 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.6→2.69 Å / Rmerge(I) obs: 0.507 / Num. unique all: 1378 / % possible all: 55.3 |
Reflection shell | *PLUS % possible obs: 55.3 % / Redundancy: 1.2 % |
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Processing
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Refinement | Resolution: 2.6→40 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh&Huber Details: WHILE ALL OBSERVED DATA OUT TO 2.6 ANGSTROM HAS BEEN USED IN REFINEMENT, THE NOMINAL RESOLUTION OF THE STRUCTURE IS 2.8 ANGSTROM
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Displacement parameters | Biso mean: 27.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
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Software | *PLUS Name: X-PLOR(ONLINE) / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 10.3 % / Rfactor obs: 0.207 / Rfactor Rfree: 0.278 | ||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 27.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.32 / % reflection Rfree: 12.3 % / Rfactor Rwork: 0.267 |