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Yorodumi- PDB-3fcc: CRYSTAL STRUCTURE OF DLTA PROTEIN IN COMPLEX WITH ATP and MAGNESIUM -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fcc | ||||||
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Title | CRYSTAL STRUCTURE OF DLTA PROTEIN IN COMPLEX WITH ATP and MAGNESIUM | ||||||
Components | D-alanine--poly(phosphoribitol) ligase subunit 1 | ||||||
Keywords | LIGASE / DLTA / AMP-FORMING DOMAIN / D-ALANINE / ADENYLATION / D-ALANINE CARRIER PROTEIN LIGASE / ATP complex | ||||||
Function / homology | Function and homology information 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 | Bacillus cereus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å | ||||||
Authors | Osman, K.T. / Du, L. / He, Y. / Luo, Y. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fcc.cif.gz | 115.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fcc.ent.gz | 86.9 KB | Display | PDB format |
PDBx/mmJSON format | 3fcc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/3fcc ftp://data.pdbj.org/pub/pdb/validation_reports/fc/3fcc | HTTPS FTP |
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-Related structure data
Related structure data | 3fceC 3dhvS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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 Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 14579 / Gene: BC_1372, dltA / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-ROSETTA2 (DE3) / References: UniProt: Q81G39, EC: 6.1.1.13 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ATP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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 MAGNESIUM CHLORIDE, 16% PEG 3350, 21% sucrose, PH 7.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294.0K, pH 7.20 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.5418 / Wavelength: 0.97 Å | |||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 1, 2008 / Details: MIRRORS | |||||||||
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2→20 Å / Num. all: 28061 / Num. obs: 25327 / % possible obs: 90.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.092 / Rsym value: 0.092 | |||||||||
Reflection shell | Resolution: 2.23→2.29 Å / Redundancy: 2 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 4.9 / Rsym value: 0.398 / % possible all: 45.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DHV Resolution: 2.32→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.32→20 Å
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Refine LS restraints |
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