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Yorodumi- PDB-3l1a: Structural ordering of disordered ligand binding loops of biotin ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3l1a | ||||||
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Title | Structural ordering of disordered ligand binding loops of biotin protein ligase into active conformations as a consequence of dehydration | ||||||
Components | BirA bifunctional protein | ||||||
Keywords | LIGASE / Biotin protein ligase / dehydrated crystals | ||||||
Function / homology | Function and homology information biotin-protein ligase activity / biotin-[biotin carboxyl-carrier protein] ligase / biotin-[acetyl-CoA-carboxylase] ligase activity / small molecule binding / post-translational protein modification Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.69 Å | ||||||
Authors | Gupta, V. | ||||||
Citation | Journal: Plos One / Year: 2010 Title: Structural ordering of disordered ligand-binding loops of biotin protein ligase into active conformations as a consequence of dehydration. Authors: Gupta, V. / Gupta, R.K. / Khare, G. / Salunke, D.M. / Surolia, A. / Tyagi, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3l1a.cif.gz | 102.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l1a.ent.gz | 78.1 KB | Display | PDB format |
PDBx/mmJSON format | 3l1a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l1/3l1a ftp://data.pdbj.org/pub/pdb/validation_reports/l1/3l1a | HTTPS FTP |
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-Related structure data
Related structure data | 3l2zC 2cghS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 28153.027 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: birA, MT3379, Rv3279c / Plasmid: pASK-IBA43plus / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: P96884, biotin-[biotin carboxyl-carrier protein] ligase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 12-16% PEG 4000, PEG 8000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE |
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: 2.69→23.989 Å / Num. obs: 13250 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 2.69→2.82 Å / Redundancy: 3.25 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 2.1 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2CGH Resolution: 2.69→23.989 Å / SU ML: 0.79 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 32.69 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.107 Å2 / ksol: 0.316 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.69→23.989 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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