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- PDB-3dwk: Identification of Dynamic Structural Motifs Involved in Peptidogl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3dwk | ||||||
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Title | Identification of Dynamic Structural Motifs Involved in Peptidoglycan Glycosyltransfer | ||||||
![]() | Penicillin-binding protein 2 | ||||||
![]() | TRANSFERASE / lysozyme-fold transpeptidase fold pi-helix / Cell shape / Cell wall biogenesis/degradation / Membrane / Peptidoglycan synthesis | ||||||
Function / homology | ![]() peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / membrane => GO:0016020 Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Lovering, A.L. / De Castro, L. / Strynadka, N.C.J. | ||||||
![]() | ![]() Title: Identification of dynamic structural motifs involved in peptidoglycan glycosyltransfer. Authors: Lovering, A.L. / De Castro, L. / Strynadka, N.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 426.3 KB | Display | ![]() |
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PDB format | ![]() | 355.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 507.2 KB | Display | ![]() |
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Full document | ![]() | 584.8 KB | Display | |
Data in XML | ![]() | 90.7 KB | Display | |
Data in CIF | ![]() | 121.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2olvS S: Starting model for refinement |
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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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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 69626.914 Da / Num. of mol.: 4 / Fragment: PBP2 (UNP residues 68-692) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-LDA / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.44 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100mM Hepes pH 7.5 2M Ammonium Sulphate 0.28mM LDAO, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2006 |
Radiation | Monochromator: Double crystal, Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96649 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→41.88 Å / Num. all: 63100 / Num. obs: 60450 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rsym value: 0.119 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 3.1→3.27 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 1.9 / % possible all: 92.4 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2OLV Resolution: 3.1→41.88 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 317.12 Å2 / Biso mean: 72.405 Å2 / Biso min: 8.12 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→41.88 Å
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