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Yorodumi- PDB-2uzf: Crystal structure of Staphylococcus aureus 1,4-dihydroxy-2-naphth... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2uzf | ||||||
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Title | Crystal structure of Staphylococcus aureus 1,4-dihydroxy-2-naphthoyl CoA synthase (MenB) in complex with acetoacetyl CoA | ||||||
Components | NAPHTHOATE SYNTHASE | ||||||
Keywords | LYASE / MENAQUINONE BIOSYNTHESIS | ||||||
Function / homology | Function and homology information 1,4-dihydroxy-2-naphthoyl-CoA synthase / 1,4-dihydroxy-2-naphthoyl-CoA synthase activity / menaquinone biosynthetic process Similarity search - Function | ||||||
Biological species | STAPHYLOCOCCUS AUREUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Ulaganathan, V. / Buetow, L. / Hunter, W.N. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2007 Title: Structure of Staphylococcus Aureus1,4-Dihydroxy-2-Naphthoyl-Coa Synthase (Menb) in Complex with Acetoacetyl-Coa. Authors: Ulaganathan, V. / Agacan, M.F. / Buetow, L. / Tulloch, L.B. / Hunter, W.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2uzf.cif.gz | 113.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2uzf.ent.gz | 87.4 KB | Display | PDB format |
PDBx/mmJSON format | 2uzf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2uzf_validation.pdf.gz | 685.3 KB | Display | wwPDB validaton report |
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Full document | 2uzf_full_validation.pdf.gz | 698 KB | Display | |
Data in XML | 2uzf_validation.xml.gz | 21.9 KB | Display | |
Data in CIF | 2uzf_validation.cif.gz | 29.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/2uzf ftp://data.pdbj.org/pub/pdb/validation_reports/uz/2uzf | HTTPS FTP |
-Related structure data
Related structure data | 1q52S 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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Unit cell |
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-Components
#1: Protein | Mass: 30462.584 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q5HH38, 1,4-dihydroxy-2-naphthoyl-CoA synthase #2: Chemical | ChemComp-CAA / | #3: 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: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE |
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Crystal grow | pH: 7.7 Details: 0.1M NA HEPES PH 7.5 1.6M AMMONIUM SULPHATE 0.2M SODIUM CHLORIDE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 20, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→84.82 Å / Num. obs: 13061 / % possible obs: 100 % / Observed criterion σ(I): 1.7 / Redundancy: 3.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Q52 Resolution: 2.9→84.82 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.813 / SU B: 50.171 / SU ML: 0.485 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.559 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.41 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→84.82 Å
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Refine LS restraints |
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