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Yorodumi- PDB-5sxy: The solution NMR structure for the PqqD truncation of Methylobact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5sxy | |||||||||
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Title | The solution NMR structure for the PqqD truncation of Methylobacterium extorquens PqqCD representing a functional and stand-alone ribosomally synthesized and post-translational modified (RiPP) recognition element (RRE) | |||||||||
Components | Bifunctional coenzyme PQQ synthesis protein C/D | |||||||||
Keywords | CHAPERONE / RiPP RRE peptide scaffolding | |||||||||
Function / homology | Function and homology information pyrroloquinoline-quinone synthase activity / pyrroloquinoline-quinone synthase / pyrroloquinoline quinone biosynthetic process / sulfur compound metabolic process / quinone binding Similarity search - Function | |||||||||
Biological species | Methylobacterium extorquens (bacteria) | |||||||||
Method | SOLUTION NMR / simulated annealing | |||||||||
Authors | Evans, R.L. / Xia, Y. / Wilmot, C.M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Biochemistry / Year: 2017 Title: Nuclear Magnetic Resonance Structure and Binding Studies of PqqD, a Chaperone Required in the Biosynthesis of the Bacterial Dehydrogenase Cofactor Pyrroloquinoline Quinone. Authors: Evans, R.L. / Latham, J.A. / Xia, Y. / Klinman, J.P. / Wilmot, C.M. #1: Journal: to be published Title: 1H, 13C, and 15N resonance assignments and secondary structure information for Methylobacterium extorquens PqqD and the complex of PqqD with PqqA Authors: Evans, R.L. / Latham, J.A. / Klinman, J.P. / Wilmot, C.M. / Xia, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5sxy.cif.gz | 571.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5sxy.ent.gz | 479.7 KB | Display | PDB format |
PDBx/mmJSON format | 5sxy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5sxy_validation.pdf.gz | 401.9 KB | Display | wwPDB validaton report |
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Full document | 5sxy_full_validation.pdf.gz | 515.7 KB | Display | |
Data in XML | 5sxy_validation.xml.gz | 28.8 KB | Display | |
Data in CIF | 5sxy_validation.cif.gz | 48.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sx/5sxy ftp://data.pdbj.org/pub/pdb/validation_reports/sx/5sxy | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 10421.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methylobacterium extorquens (strain ATCC 14718 / DSM 1338 / AM1) (bacteria) Strain: ATCC 14718 / DSM 1338 / AM1 / Gene: pqqCD, MexAM1_META1p1749 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q49150, pyrroloquinoline-quinone synthase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution / Contents: 4.6 mg/mL [U-13C; U-15N] PqqD, 95% H2O/5% D2O Details: PqqD sample contained 285 micro-L of 5.0 mg/ml (0.40 mM) 13C-, 15N-labeled M.ex.PqqD in 25 mM potassium phosphate, pH 6.5, 7 micro-L of 50 mM sodium azide, and 15 micro-L HPLC grade D2O. ...Details: PqqD sample contained 285 micro-L of 5.0 mg/ml (0.40 mM) 13C-, 15N-labeled M.ex.PqqD in 25 mM potassium phosphate, pH 6.5, 7 micro-L of 50 mM sodium azide, and 15 micro-L HPLC grade D2O. Final concentrations: 4.6 mg/ml (0.37 mM) MexPqqD, 1.1 mM sodium azide, 4.9% D2O). Label: PqqD / Solvent system: 95% H2O/5% D2O |
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Sample | Conc.: 4.6 mg/mL / Component: PqqD / Isotopic labeling: [U-13C; U-15N] |
Sample conditions | Details: PqqD sample contained 285 micro-L of 5.0 mg/ml (0.40 mM) 13C-, 15N-labeled M.ex.PqqD in 25 mM potassium phosphate, pH 6.5, 7 micro-L of 50 mM sodium azide, and 15 micro-L HPLC grade D2O. ...Details: PqqD sample contained 285 micro-L of 5.0 mg/ml (0.40 mM) 13C-, 15N-labeled M.ex.PqqD in 25 mM potassium phosphate, pH 6.5, 7 micro-L of 50 mM sodium azide, and 15 micro-L HPLC grade D2O. Final concentrations: 4.6 mg/ml (0.37 mM) MexPqqD, 1.1 mM sodium azide, 4.9% D2O). Ionic strength: 25 mM / Label: PqqD / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 6 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |