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Yorodumi- PDB-3qxh: Crystal structure of dethiobiotin synthetase (BioD) from Helicoba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qxh | ||||||
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Title | Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with ADP and 8-aminocaprylic acid | ||||||
Components | Dethiobiotin synthetase | ||||||
Keywords | LIGASE / DTBS / DETHIOBIOTIN SYNTHETASE / ATP 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: 1.36 Å | ||||||
Authors | Porebski, P.J. / Klimecka, M.M. / Chruszcz, M. / Murzyn, K. / Minor, C. / 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 | 3qxh.cif.gz | 117.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qxh.ent.gz | 88 KB | Display | PDB format |
PDBx/mmJSON format | 3qxh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qxh_validation.pdf.gz | 799.9 KB | Display | wwPDB validaton report |
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Full document | 3qxh_full_validation.pdf.gz | 799.9 KB | Display | |
Data in XML | 3qxh_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 3qxh_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/3qxh ftp://data.pdbj.org/pub/pdb/validation_reports/qx/3qxh | HTTPS FTP |
-Related structure data
Related structure data | 2qmoSC 3mleC 3qxcC 3qxjC 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 , 6 types, 363 molecules
#2: Chemical | ChemComp-8AC / | ||||||
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#3: Chemical | ChemComp-ADP / | ||||||
#4: Chemical | #5: Chemical | ChemComp-PO4 / | #6: Chemical | ChemComp-EDO / #7: 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: 36.07 % |
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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 ATP, 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 / 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: 1.36→50 Å / Num. all: 43544 / Num. obs: 43544 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 11 Å2 / Rmerge(I) obs: 0.026 / Rsym value: 0.026 / Net I/σ(I): 47.3 |
Reflection shell | Resolution: 1.36→1.38 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 13.2 / Num. unique all: 1735 / Rsym value: 0.07 / % possible all: 81.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2QMO Resolution: 1.36→50 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.061 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.047 / 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: 8.869 Å2
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Refinement step | Cycle: LAST / Resolution: 1.36→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.36→1.395 Å / Total num. of bins used: 20
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