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Yorodumi- PDB-7pcm: BurG (holo) in complex with (Z)-2,3-dihydroxy-6-methyl-hept-2-eno... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pcm | ||||||
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Title | BurG (holo) in complex with (Z)-2,3-dihydroxy-6-methyl-hept-2-enoate (13): Biosynthesis of cyclopropanol rings in bacterial toxins | ||||||
Components | Ketol-acid reductoisomerase | ||||||
Keywords | LYASE / Pathogens / Natural Products / Toxins / Biosynthesis / Catalysis | ||||||
Function / homology | Function and homology information ketol-acid reductoisomerase (NADP+) / ketol-acid reductoisomerase activity / valine biosynthetic process / isoleucine biosynthetic process / amino acid biosynthetic process / nucleotide binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Burkholderia thailandensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Trottmann, F. / Ishida, K. / Ishida, M. / Kries, H. / Groll, M. / Hertweck, C. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Nat.Chem. / Year: 2022 Title: Pathogenic bacteria remodel central metabolic enzyme to build a cyclopropanol warhead. Authors: Trottmann, F. / Ishida, K. / Ishida-Ito, M. / Kries, H. / Groll, M. / Hertweck, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pcm.cif.gz | 278.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pcm.ent.gz | 224 KB | Display | PDB format |
PDBx/mmJSON format | 7pcm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pcm_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 7pcm_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 7pcm_validation.xml.gz | 26.1 KB | Display | |
Data in CIF | 7pcm_validation.cif.gz | 35.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pc/7pcm ftp://data.pdbj.org/pub/pdb/validation_reports/pc/7pcm | HTTPS FTP |
-Related structure data
Related structure data | 7pccSC 7pceC 7pcgC 7pciC 7pclC 7pcnC 7pcoC 7pctC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 38716.699 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CIP 106301 / E264) (bacteria) Strain: ATCC 700388 / DSM 13276 / CIP 106301 / E264 / Gene: ilvC-2, BTH_II2094 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q2T3G7, ketol-acid reductoisomerase (NADP+) |
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-Non-polymers , 5 types, 120 molecules
#2: Chemical | #3: Chemical | ChemComp-MG / #4: Chemical | #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.06 Å3/Da / Density % sol: 40.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris; 0.8 M LiCl, 8% PEG 4K, 2 mM NAD+, 5 mM MgCl2, 2 mM 13 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 28, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→30 Å / Num. obs: 40243 / % possible obs: 98.5 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.05→2.15 Å / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 5297 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7PCC Resolution: 2.05→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / SU B: 14.123 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 71.49 Å2 / Biso mean: 28.561 Å2 / Biso min: 16.24 Å2
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Refinement step | Cycle: final / Resolution: 2.05→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Rfactor Rfree error: 0 / 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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