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Yorodumi- PDB-2msn: NMR structure of a putative phosphoglycolate phosphatase (NP_3464... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2msn | ||||||
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Title | NMR structure of a putative phosphoglycolate phosphatase (NP_346487.1) from Streptococcus pneumoniae TIGR4 | ||||||
Components | Hydrolase, haloacid dehalogenase-like family | ||||||
Keywords | HYDROLASE / PSI-Biology / Joint Center for Structural Genomics / JCSG | ||||||
Function / homology | Function and homology information phosphoglycolate phosphatase activity / hydrolase activity / DNA repair / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae TIGR4 (bacteria) | ||||||
Method | SOLUTION NMR / torsion angle dynamics, simulated annealing | ||||||
Model details | closest to the average, model1 | ||||||
Authors | Jaudzems, K. / Serrano, P. / Pedrini, B. / Geralt, M. / Wuthrich, K. / Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: J.Biomol.Nmr / Year: 2015 Title: J-UNIO protocol used for NMR structure determination of the 206-residue protein NP_346487.1 from Streptococcus pneumoniae TIGR4. Authors: Jaudzems, K. / Pedrini, B. / Geralt, M. / Serrano, P. / Wuthrich, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2msn.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2msn.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 2msn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2msn_validation.pdf.gz | 414.2 KB | Display | wwPDB validaton report |
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Full document | 2msn_full_validation.pdf.gz | 540.7 KB | Display | |
Data in XML | 2msn_validation.xml.gz | 80.6 KB | Display | |
Data in CIF | 2msn_validation.cif.gz | 105.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ms/2msn ftp://data.pdbj.org/pub/pdb/validation_reports/ms/2msn | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 23706.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae TIGR4 (bacteria) Strain: TIGR4 / Gene: SP_2064 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 References: UniProt: Q97NG6, UniProt: A0A0H2URV7*PLUS, phosphoglycolate phosphatase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.5 mM [U-100% 13C; U-100% 15N] protein, 5 % [U-100% 2H] D2O, 0.03 % sodium azide, 20 mM sodium phosphate, 50 mM sodium chloride, 95% H2O/5% D2O Solvent system: 95% H2O/5% D2O | ||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.08 / pH: 6.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics, simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 4222 / NOE intraresidue total count: 1008 / NOE long range total count: 1046 / NOE medium range total count: 1037 / NOE sequential total count: 1051 | ||||||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |