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Yorodumi- PDB-5fm0: Crystal structure of the 6-carboxyhexanoate-CoA ligase (BioW)from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fm0 | ||||||
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Title | Crystal structure of the 6-carboxyhexanoate-CoA ligase (BioW)from Bacillus subtilis (PtCl4 derivative) | ||||||
Components | 6-CARBOXYHEXANOATE--COA LIGASE | ||||||
Keywords | LIGASE | ||||||
Function / homology | Function and homology information 6-carboxyhexanoate-CoA ligase / 6-carboxyhexanoate-CoA ligase activity / biotin biosynthetic process / magnesium ion binding / ATP binding Similarity search - Function | ||||||
Biological species | BACILLUS SUBTILIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.44 Å | ||||||
Authors | Moynie, L. / Wang, M. / Campopiano, D.J. / Naismith, J.H. | ||||||
Citation | Journal: Nat. Chem. Biol. / Year: 2017 Title: Using the pimeloyl-CoA synthetase adenylation fold to synthesize fatty acid thioesters. Authors: Wang, M. / Moynie, L. / Harrison, P.J. / Kelly, V. / Piper, A. / Naismith, J.H. / Campopiano, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fm0.cif.gz | 115.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fm0.ent.gz | 89 KB | Display | PDB format |
PDBx/mmJSON format | 5fm0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fm0_validation.pdf.gz | 901.9 KB | Display | wwPDB validaton report |
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Full document | 5fm0_full_validation.pdf.gz | 908 KB | Display | |
Data in XML | 5fm0_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 5fm0_validation.cif.gz | 26.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/5fm0 ftp://data.pdbj.org/pub/pdb/validation_reports/fm/5fm0 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 6 - 255 / Label seq-ID: 7 - 256
NCS oper: (Code: given Matrix: (0.2919, 0.9526, -0.0862), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 29674.422 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P53559, 6-carboxyhexanoate-CoA ligase |
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-Non-polymers , 5 types, 30 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PT / #6: 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: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 0.1 MM HEPES PH 7.5 19 % PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.07206 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 6, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07206 Å / Relative weight: 1 |
Reflection | Resolution: 2.44→83.35 Å / Num. obs: 25521 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 15.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 2.44→2.5 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 3.3 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.44→83.35 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.936 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.358 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.428 Å2
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Refinement step | Cycle: LAST / Resolution: 2.44→83.35 Å
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Refine LS restraints |
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