+Open data
-Basic information
Entry | Database: PDB / ID: 4qii | ||||||
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Title | Crystal Structure of type II MenB from Mycobacteria tuberculosis | ||||||
Components | 1,4-Dihydroxy-2-naphthoyl-CoA synthase | ||||||
Keywords | LYASE / 1 / 4-dihydroxy-2-naphthoyl-coenzyme A / synthase | ||||||
Function / homology | Function and homology information 1,4-dihydroxy-2-naphthoyl-CoA synthase / 1,4-dihydroxy-2-naphthoyl-CoA synthase activity / menaquinone biosynthetic process / protein hexamerization / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å | ||||||
Authors | Song, H.G. / Tse, Y.S. / Sung, H.P. / Guo, Z.H. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Ligand-dependent active-site closure revealed in the crystal structure of Mycobacterium tuberculosis MenB complexed with product analogues Authors: Song, H. / Sung, H.P. / Tse, Y.S. / Jiang, M. / Guo, Z.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qii.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4qii.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 4qii.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qii_validation.pdf.gz | 3.6 MB | Display | wwPDB validaton report |
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Full document | 4qii_full_validation.pdf.gz | 3.7 MB | Display | |
Data in XML | 4qii_validation.xml.gz | 169.5 KB | Display | |
Data in CIF | 4qii_validation.cif.gz | 242.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/4qii ftp://data.pdbj.org/pub/pdb/validation_reports/qi/4qii | HTTPS FTP |
-Related structure data
Related structure data | 4qijC 1q52S C: citing same article (ref.) S: Starting model for refinement |
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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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-Components
#1: Protein | Mass: 36903.301 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P9WNP5, 1,4-dihydroxy-2-naphthoyl-CoA synthase #2: Chemical | ChemComp-2NE / #3: Chemical | ChemComp-PGE / #4: 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 | Density Matthews: 2.09 Å3/Da / Density % sol: 41.13 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2M NaCl, 0.1M HEPES pH 8.5, 25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→34.96 Å / Num. obs: 439236 / Biso Wilson estimate: 16.5 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Q52 Resolution: 1.64→34.955 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 18.1 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.64→34.955 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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Refinement TLS params. | Method: refined / Origin x: 158.7066 Å / Origin y: 6.1818 Å / Origin z: 210.0187 Å
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Refinement TLS group | Selection details: all |