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Yorodumi- PDB-3qxj: Crystal structure of dethiobiotin synthetase (BioD) from Helicoba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qxj | ||||||
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Title | Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with GTP | ||||||
Components | Dethiobiotin synthetase | ||||||
Keywords | LIGASE / DTBS / dethiobiotin synthetase / ADP binding / Structural Genomics / PSI-BIOLOGY / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information dethiobiotin synthase / dethiobiotin synthase activity / biotin biosynthetic process / magnesium ion binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å | ||||||
Authors | Klimecka, M.M. / Porebski, P.J. / Chruszcz, M. / Murzyn, K. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: Febs J. / Year: 2012 Title: Structural characterization of Helicobacter pylori dethiobiotin synthetase reveals differences between family members. Authors: Porebski, P.J. / Klimecka, M. / Chruszcz, M. / Nicholls, R.A. / Murzyn, K. / Cuff, M.E. / Xu, X. / Cymborowski, M. / Murshudov, G.N. / Savchenko, A. / Edwards, A. / Minor, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qxj.cif.gz | 114.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qxj.ent.gz | 86.3 KB | Display | PDB format |
PDBx/mmJSON format | 3qxj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qxj_validation.pdf.gz | 777 KB | Display | wwPDB validaton report |
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Full document | 3qxj_full_validation.pdf.gz | 778.5 KB | Display | |
Data in XML | 3qxj_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 3qxj_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/3qxj ftp://data.pdbj.org/pub/pdb/validation_reports/qx/3qxj | HTTPS FTP |
-Related structure data
Related structure data | 2qmoSC 3mleC 3qxcC 3qxhC 3qxsC 3qxxC 3qy0C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 27148.088 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: bioD, hp0029, HP_0029 / Plasmid: p11 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 Gold(de3) Magic / References: UniProt: O24872, dethiobiotin synthase |
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-Non-polymers , 5 types, 313 molecules
#2: Chemical | ChemComp-GTP / | ||||||
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#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-MG / | #5: Chemical | ChemComp-NO3 / | #6: 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: 1.92 Å3/Da / Density % sol: 36.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 20% PEG3350; 150 MM NH4NO3; 100 MM, BIS-TRIS; SOAKED WITH 10 MM GTP, 10 MM MGCL2, 10 MM 8-AMINOOCTANOIC ACID; IN SITU PROTEOLYSIS - CHYMOTRYPSIN, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Jul 11, 2008 / Details: MIRROR |
Radiation | Monochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.38→50 Å / Num. all: 42504 / Num. obs: 42504 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 35.8 |
Reflection shell | Resolution: 1.38→1.4 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1929 / Rsym value: 0.4 / % possible all: 90.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2QMO Resolution: 1.38→50 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.791 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.199 Å2
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Refinement step | Cycle: LAST / Resolution: 1.38→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.38→1.416 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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