+Open data
-Basic information
Entry | Database: PDB / ID: 2klm | ||||||
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Title | Solution Structure of L11 with SAXS and RDC | ||||||
Components | 50S ribosomal protein L11 | ||||||
Keywords | RIBOSOMAL PROTEIN / L11 / RDC / SAXS / Methylation / Ribonucleoprotein / RNA-binding / rRNA-binding | ||||||
Function / homology | Function and homology information large ribosomal subunit rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | SOLUTION SCATTERING / SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Wang, J. / Zuo, X. / Yu, P. / Schwieters, C.D. / Wang, Y. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2009 Title: Determination of multicomponent protein structures in solution using global orientation and shape restraints. Authors: Wang, J. / Zuo, X. / Yu, P. / Byeon, I.J. / Jung, J. / Wang, X. / Dyba, M. / Seifert, S. / Schwieters, C.D. / Qin, J. / Gronenborn, A.M. / Wang, Y.X. #1: Journal: J. Mol. Biol. / Year: 2007 Title: The Structure of Free L11 and Functional Dynamics of L11 in Free, L11-rRNA(58nt) Binary and L11-rRNA(58nt)-thiostrepton Ternary Complexes Authors: Lee, D. / Walsh, J. / Yu, P. / Markus, M. / Choli-papadopoulou, T. / Schwieters, C. / Krueger, S. / Draper, D. / Wang, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2klm.cif.gz | 446.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2klm.ent.gz | 372.4 KB | Display | PDB format |
PDBx/mmJSON format | 2klm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2klm_validation.pdf.gz | 345.3 KB | Display | wwPDB validaton report |
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Full document | 2klm_full_validation.pdf.gz | 451.3 KB | Display | |
Data in XML | 2klm_validation.xml.gz | 39.1 KB | Display | |
Data in CIF | 2klm_validation.cif.gz | 52.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kl/2klm ftp://data.pdbj.org/pub/pdb/validation_reports/kl/2klm | 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: 15526.111 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: rplK, rpl11 / Production host: Escherichia coli (E. coli) / References: UniProt: P36238 |
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-Experimental details
-Experiment
Experiment |
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NMR experiment | Type: 2D 1H-15N HSQC |
-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 0.2 / pH: 6.5 / Pressure: ambient / Temperature: 298 K |
-Data collection
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz |
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Soln scatter | Type: x-ray / Buffer name: 50 MM NACL 20 MM MES / Conc. range: 1.0-5.0 / Data analysis software list: GNOM Data reduction software list: MARDETECTOR, HOME- WRITTEN PROGRAM Detector specific: HOME-MADE / Detector type: CCD CAMERA / Mean guiner radius: 2.05 nm / Mean guiner radius esd: 0.03 nm / Num. of time frames: 20 / Protein length: 0.5 / Sample pH: 6.5 / Source beamline: 12-ID / Source class: Y / Source type: APS ARGONNE / Temperature: 298 K |
-Processing
NMR software | Name: X-PLOR NIH / Developer: Schwieters, Kuszewski, Tjandra and Clore / Classification: refinement |
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Refinement | Method: simulated annealing / Software ordinal: 1 |
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: 10 |
Soln scatter model | Conformer selection criteria: STRUCTURES WITH THE LOWEST ENERGY Num. of conformers calculated: 100 / Num. of conformers submitted: 10 / Representative conformer: 1 / Software list: GNOM |