[English] 日本語
Yorodumi- PDB-1byi: STRUCTURE OF APO-DETHIOBIOTIN SYNTHASE AT 0.97 ANGSTROMS RESOLUTION -
+Open data
-Basic information
Entry | Database: PDB / ID: 1byi | ||||||
---|---|---|---|---|---|---|---|
Title | STRUCTURE OF APO-DETHIOBIOTIN SYNTHASE AT 0.97 ANGSTROMS RESOLUTION | ||||||
Components | DETHIOBIOTIN SYNTHASE | ||||||
Keywords | LIGASE / BIOTIN SYNTHESIS / CYCLO-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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.97 Å | ||||||
Authors | Sandalova, T. / Schneider, G. / Kaeck, H. / Lindqvist, Y. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Structure of dethiobiotin synthetase at 0.97 A resolution. Authors: Sandalova, T. / Schneider, G. / Kack, H. / Lindqvist, Y. #1: Journal: Structure / Year: 1994 Title: Crystal Structure of an ATP-Dependent Carboxylase, Dethiobiotin Synthetase, at 1.65 A Resolution Authors: Huang, W. / Lindqvist, Y. / Schneider, G. / Gibson, K.J. / Flint, D. / Lorimer, G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1byi.cif.gz | 120.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1byi.ent.gz | 94.5 KB | Display | PDB format |
PDBx/mmJSON format | 1byi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1byi_validation.pdf.gz | 408.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1byi_full_validation.pdf.gz | 413.3 KB | Display | |
Data in XML | 1byi_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 1byi_validation.cif.gz | 25 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/1byi ftp://data.pdbj.org/pub/pdb/validation_reports/by/1byi | HTTPS FTP |
-Related structure data
Related structure data | 1dtsS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 24028.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P13000, dethiobiotin synthase |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 6.5 / Details: pH 6.5 | |||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6 / Method: microdialysis | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9082 |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9082 Å / Relative weight: 1 |
Reflection | Resolution: 0.97→15 Å / Num. obs: 116232 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.025 / Net I/σ(I): 54.4 |
Reflection shell | Resolution: 0.97→0.98 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 4.2 / Rsym value: 0.245 / % possible all: 94.3 |
Reflection | *PLUS Num. measured all: 494742 |
Reflection shell | *PLUS % possible obs: 94.3 % / Rmerge(I) obs: 0.245 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DTS Resolution: 0.97→15 Å / Num. parameters: 20493 / Num. restraintsaints: 25635 / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
| |||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: MOEWS & KRETSINGER | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 79 / Occupancy sum hydrogen: 1684.4 / Occupancy sum non hydrogen: 2075 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.97→15 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_chiral_restr / Dev ideal: 0.078 |