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- PDB-3fce: Crystal Structure of Bacillus cereus D-alanyl Carrier Protein Lig... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3fce | ||||||
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Title | Crystal Structure of Bacillus cereus D-alanyl Carrier Protein Ligase DltA in Complex with ATP: Implications for Adenylation Mechanism | ||||||
![]() | D-alanine--poly(phosphoribitol) ligase subunit 1 | ||||||
![]() | LIGASE / DLTA / AMP-FORMING DOMAIN / D-ALANINE / ADENYLATION / D-ALANINE CARRIER PROTEIN LIGASE / ATP Complex | ||||||
Function / homology | ![]() D-alanine-[D-alanyl-carrier protein] ligase / D-alanine [D-alanyl carrier protein] ligase activity / lipoteichoic acid biosynthetic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Osman, K.T. / Du, L. / He, Y. / Luo, Y. | ||||||
![]() | ![]() Title: Crystal structure of Bacillus cereus D-alanyl carrier protein ligase (DltA) in complex with ATP. Authors: Osman, K.T. / Du, L. / He, Y. / Luo, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 123.2 KB | Display | ![]() |
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PDB format | ![]() | 92.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 759.1 KB | Display | ![]() |
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Full document | ![]() | 772.1 KB | Display | |
Data in XML | ![]() | 25.1 KB | Display | |
Data in CIF | ![]() | 37.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3fccC ![]() 3dhvS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 57625.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: DltA was expressed as a fusion protein with C-terminal Histag. Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-ATP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.88 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 0.05 M HEPES, 0.2 M POTASSIUM CHLORIDE, 0.1 M CALCIUM CHLORIDE, 16% PEG 3350, 21% sucrose, PH 7.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Oct 25, 2008 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. all: 44062 / Num. obs: 38547 / % possible obs: 87.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 |
Reflection shell | Resolution: 1.9→2.02 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 2 / Rsym value: 0.306 / % possible all: 44.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3DHV Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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