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Yorodumi- PDB-1a82: DETHIOBIOTIN SYNTHETASE FROM ESCHERICHIA COLI, COMPLEX WITH SUBST... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a82 | |||||||||
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Title | DETHIOBIOTIN SYNTHETASE FROM ESCHERICHIA COLI, COMPLEX WITH SUBSTRATES ATP AND DIAMINOPELARGONIC ACID | |||||||||
Components | DETHIOBIOTIN SYNTHETASE | |||||||||
Keywords | BIOTIN BIOSYNTHESIS / PHOSPHORYL TRANSFER / LIGASE | |||||||||
Function / homology | Function and homology information dethiobiotin synthase / dethiobiotin synthase activity / biotin biosynthetic process / magnesium ion binding / protein homodimerization activity / ATP binding / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 1.8 Å | |||||||||
Authors | Kaeck, H. / Gibson, K.J. / Lindqvist, Y. / Schneider, G. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1998 Title: Snapshot of a phosphorylated substrate intermediate by kinetic crystallography. Authors: Kack, H. / Gibson, K.J. / Lindqvist, Y. / Schneider, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a82.cif.gz | 62.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a82.ent.gz | 43.7 KB | Display | PDB format |
PDBx/mmJSON format | 1a82.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a82_validation.pdf.gz | 465.1 KB | Display | wwPDB validaton report |
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Full document | 1a82_full_validation.pdf.gz | 466.8 KB | Display | |
Data in XML | 1a82_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | 1a82_validation.cif.gz | 10.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a8/1a82 ftp://data.pdbj.org/pub/pdb/validation_reports/a8/1a82 | HTTPS FTP |
-Related structure data
Related structure data | 1dakC 1dahS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 24028.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Cellular location: CYTOPLASM / Cellular location (production host): CYTOPLASM / Gene (production host): BIOD / Production host: Escherichia coli (E. coli) / References: UniProt: P13000, dethiobiotin synthase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-DNN / |
#4: Chemical | ChemComp-ATP / |
#5: 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: 2.15 Å3/Da / Density % sol: 43 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusionDetails: drop contained 0.003ml of protein solution mixed with 0.074ml of well solution. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1997 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 18671 / % possible obs: 98.7 % / Redundancy: 2.5 % / Biso Wilson estimate: 11.9 Å2 / Rsym value: 0.03 / Net I/σ(I): 25.6 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 7 / Rsym value: 0.116 / % possible all: 93.5 |
Reflection | *PLUS Num. measured all: 47020 / Rmerge(I) obs: 0.03 |
Reflection shell | *PLUS % possible obs: 93.5 % / Rmerge(I) obs: 0.116 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: PDB ENTRY 1DAH, WITH NON-PROTEIN ATOMS EXCLUDED Resolution: 1.8→20 Å / Rfactor Rfree error: 0.008 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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