+Open data
-Basic information
Entry | Database: PDB / ID: 2lss | ||||||
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Title | Solution structure of the R. rickettsii cold shock-like protein | ||||||
Components | Cold shock-like protein | ||||||
Keywords | RNA BINDING PROTEIN / DNA BINDING PROTEIN / cold shock-like protein / CSD / Csp / oligonucleotide binding fold / OB fold | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Rickettsia rickettsii (bacteria) | ||||||
Method | SOLUTION NMR / AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT. | ||||||
Authors | Veldkamp, C.T. / Peterson, F.C. / Gerarden, K.P. / Fuchs, A.M. / Koch, J.M. / Mueller, M.M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2012 Title: Solution structure of the cold-shock-like protein from Rickettsia rickettsii. Authors: Gerarden, K.P. / Fuchs, A.M. / Koch, J.M. / Mueller, M.M. / Graupner, D.R. / O'Rorke, J.T. / Frost, C.D. / Heinen, H.A. / Lackner, E.R. / Schoeller, S.J. / House, P.G. / Peterson, F.C. / Veldkamp, C.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2lss.cif.gz | 479.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2lss.ent.gz | 408.9 KB | Display | PDB format |
PDBx/mmJSON format | 2lss.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/2lss ftp://data.pdbj.org/pub/pdb/validation_reports/ls/2lss | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 7781.743 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rickettsia rickettsii (bacteria) / Strain: Sheila Smith / Gene: A1G_05630 / Plasmid: pET28a-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8GT84, UniProt: A0A0H3AYC3*PLUS |
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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] cold shock-like protein [Rickettsia rickettsii str. 'Sheila Smith'], 20 mM sodium phosphate, 50 mM sodium chloride, 0.02 % sodium azide, 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 200 / pH: 6.0 / Pressure: AMBIENT / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz |
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-Processing
NMR software |
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Refinement | Method: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT. Software ordinal: 1 Details: RR-CSP STRUCTURES ARE BASED ON A TOTAL OF 1813 NOE CONSTRAINTS (1123 INTRA, 298 SEQUENTIAL, 86 MEDIUM, 306 LONG RANGE) AND 120 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS. | ||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 1813 / NOE intraresidue total count: 1123 / NOE long range total count: 306 / NOE medium range total count: 86 / NOE sequential total count: 298 / Protein phi angle constraints total count: 60 / Protein psi angle constraints total count: 60 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |