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Yorodumi- PDB-6ojc: A high-resolution crystal structure of NocB thioesterase domain f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ojc | ||||||
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Title | A high-resolution crystal structure of NocB thioesterase domain from Nocardicin cluster | ||||||
Components | NocB | ||||||
Keywords | HYDROLASE / Nonribosomal peptide synthetase (NRPS) / thioesterase / epimerization / alpha/beta hydrolase fold | ||||||
Function / homology | Function and homology information amide biosynthetic process / organonitrogen compound biosynthetic process / secondary metabolite biosynthetic process / carboxylic acid metabolic process / lipid biosynthetic process / phosphopantetheine binding / catalytic activity Similarity search - Function | ||||||
Biological species | Nocardia uniformis subsp. tsuyamanensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.94 Å | ||||||
Authors | Patel, K.D. / Gulick, A.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2019 Title: Structure of a bound peptide phosphonate reveals the mechanism of nocardicin bifunctional thioesterase epimerase-hydrolase half-reactions. Authors: Patel, K.D. / d'Andrea, F.B. / Gaudelli, N.M. / Buller, A.R. / Townsend, C.A. / Gulick, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ojc.cif.gz | 139 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ojc.ent.gz | 109.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ojc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/6ojc ftp://data.pdbj.org/pub/pdb/validation_reports/oj/6ojc | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 27743.877 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nocardia uniformis subsp. tsuyamanensis (bacteria) Gene: nocB / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5J1Q6 | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.53 % / Description: Octahedral |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 2.0M Ammonium sulfate, 0.05M BisTris pH 5.0 / PH range: 5.0-6.0 |
-Data collection
Diffraction | Mean temperature: 113.15 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03321 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03321 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→99.37 Å / Num. obs: 26388 / % possible obs: 99.7 % / Redundancy: 9.4 % / Biso Wilson estimate: 40.76 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.024 / Rrim(I) all: 0.053 / Χ2: 1.24 / Net I/σ(I): 25.6 |
Reflection shell | Resolution: 1.79→1.83 Å / Redundancy: 9.3 % / Rmerge(I) obs: 1.54 / Mean I/σ(I) obs: 1 / Num. unique obs: 1916 / CC1/2: 0.521 / Rpim(I) all: 0.77 / Rrim(I) all: 1.72 / Χ2: 0.48 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.94→29.241 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.24 / Phase error: 25.26
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.94→29.241 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -44.7209 Å / Origin y: 14.2554 Å / Origin z: 14.85 Å
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Refinement TLS group | Selection details: all |