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Yorodumi- PDB-4fqd: Crystal structure of the enolpyruvyl transferase NikO from Strept... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fqd | ||||||
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Title | Crystal structure of the enolpyruvyl transferase NikO from Streptomyces tendae | ||||||
Components | NikO protein | ||||||
Keywords | TRANSFERASE / beta/alpha inverse barrel / enolpyruvyl transferase / fosfomycin binding | ||||||
Function / homology | Function and homology information transferase activity, transferring alkyl or aryl (other than methyl) groups Similarity search - Function | ||||||
Biological species | Streptomyces tendae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Oberdorfer, G. / Gruber, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Structural and functional characterization of NikO, an enolpyruvyl transferase essential in nikkomycin biosynthesis. Authors: Oberdorfer, G. / Binter, A. / Ginj, C. / Macheroux, P. / Gruber, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fqd.cif.gz | 179.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fqd.ent.gz | 142.9 KB | Display | PDB format |
PDBx/mmJSON format | 4fqd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fqd_validation.pdf.gz | 448.9 KB | Display | wwPDB validaton report |
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Full document | 4fqd_full_validation.pdf.gz | 454.8 KB | Display | |
Data in XML | 4fqd_validation.xml.gz | 33.7 KB | Display | |
Data in CIF | 4fqd_validation.cif.gz | 47.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fq/4fqd ftp://data.pdbj.org/pub/pdb/validation_reports/fq/4fqd | HTTPS FTP |
-Related structure data
Related structure data | 2yvwS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 51431.340 Da / Num. of mol.: 2 / Mutation: P52R, D96E, V97L, V141D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces tendae (bacteria) / Gene: nikO / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q712I1 #2: Chemical | #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: 2.15 Å3/Da / Density % sol: 42.8 % |
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Crystal grow | Temperature: 289 K / Method: microbatch / pH: 6.5 Details: 0.2 M Li Sulfate, 0.1 M Bis-Tris pH 6.5, 25% w/v PEG 3350, Microbatch, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 3, 2010 |
Radiation | Monochromator: Bartels Monochromator with dual channel cut crystals (DCCM) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→51.07 Å / Num. all: 31067 / Num. obs: 28377 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 20.22 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 5 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 6.6 / % possible all: 91.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2yvw Resolution: 2.5→47.248 Å / SU ML: 0.72 / σ(F): 1.35 / Phase error: 21.49 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 12.336 Å2 / ksol: 0.32 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.5→47.248 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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