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Yorodumi- PDB-2lp6: Refined Solution NMR Structure of the 50S ribosomal protein L35Ae... -
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-Basic information
Entry | Database: PDB / ID: 2lp6 | ||||||
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Title | Refined Solution NMR Structure of the 50S ribosomal protein L35Ae from Pyrococcus furiosus, Northeast Structural Genomics Consortium Target (NESG) PfR48 | ||||||
Components | 50S ribosomal protein L35Ae | ||||||
Keywords | RIBOSOMAL PROTEIN / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-Biology / Protein Structure Initiative | ||||||
Function / homology | Function and homology information ribosomal large subunit biogenesis / cytosolic large ribosomal subunit / cytoplasmic translation / structural constituent of ribosome Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Snyder, D.A. / Aramini, J.M. / Yu, B. / Huang, Y.J. / Xiao, R. / Cort, J.R. / Shastry, R. / Ma, L. / Liu, J. / Rost, B. ...Snyder, D.A. / Aramini, J.M. / Yu, B. / Huang, Y.J. / Xiao, R. / Cort, J.R. / Shastry, R. / Ma, L. / Liu, J. / Rost, B. / Acton, T.B. / Kennedy, M.A. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: Proteins / Year: 2012 Title: Solution NMR structure of the ribosomal protein RP-L35Ae from Pyrococcus furiosus. Authors: Snyder, D.A. / Aramini, J.M. / Yu, B. / Huang, Y.J. / Xiao, R. / Cort, J.R. / Shastry, R. / Ma, L.C. / Liu, J. / Rost, B. / Acton, T.B. / Kennedy, M.A. / Montelione, G.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2lp6.cif.gz | 671.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2lp6.ent.gz | 571.6 KB | Display | PDB format |
PDBx/mmJSON format | 2lp6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2lp6_validation.pdf.gz | 544.2 KB | Display | wwPDB validaton report |
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Full document | 2lp6_full_validation.pdf.gz | 712 KB | Display | |
Data in XML | 2lp6_validation.xml.gz | 44.1 KB | Display | |
Data in CIF | 2lp6_validation.cif.gz | 57.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lp/2lp6 ftp://data.pdbj.org/pub/pdb/validation_reports/lp/2lp6 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
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: 10826.713 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF1872, rpl35Ae / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: Q8TZV6 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: THE PROTEIN IS MONOMERIC BY GEL FILTRATION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING AND 15N T1/T2 RELAXATION. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATIC ...Text: THE PROTEIN IS MONOMERIC BY GEL FILTRATION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING AND 15N T1/T2 RELAXATION. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATIC BACKBONE RESONANCE ASSIGNMENTS WERE MADE USING AUTOASSIGN, FOLLOWED BY MANUAL SIDE CHAIN ASSIGNMENT. AUTOMATIC NOESY ASSIGNMENTS WERE DETERMINED USING CYANA 3.0. BACKBONE (PHI/PSI) DIHEDRAL ANGLE CONSTRAINTS WERE OBTAINED FROM TALOSplus, AND HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING AUTOSTRUCTURE. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING THE C-TERMINAL HIS6): BACKBONE, 98.2%, SIDE CHAIN, 90.9%, AROMATICS, 100%, STEREOSPECIFIC METHYL, 84.2%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 1 TO 91, PSVS 1.4), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 2-12,21-76,79-87: (A) RMSD (ORDERED RESIDUES): BB, 0.5, HEAVY ATOM, 1.0. (B) MOLPROBITY RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 97.0%, ADDITIONALLY ALLOWED, 3.0%, DISALLOWED, 0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.56/-1.89, ALL, -0.26/-1.54. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 15.13/-1.07 (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 1 TO 91): RECALL, 0.965, PRECISION, 0.878, F-MEASURE, 0.920, DP-SCORE, 0.784. (F) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 5. THE FINAL FOUR UNASSIGNED HISTIDINE RESIDUES IN THE C-TERMINAL AFFINITY TAG WERE NOT INCLUDED IN THE STRUCTURE CALCULATIONS AND HAVE BEEN OMITTED FROM THIS DEPOSITION. COORDINATES FOR THE FOLLOWING RESIDUES ARE NOT WELL DETERMINED [S(PHI) + S(PSI) < 1.8]: 1,13-20,77-78,88-91. |
-Sample preparation
Details |
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Sample |
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Sample conditions | pH: 6.5 / Pressure: ambient / Temperature: 293 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: THE FINAL REFINED STRUCTURES ARE BASED ON A TOTAL OF 1402 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 153 DIHEDRAL ANGLE CONSTRAINTS, AND 56 HYDROGEN BOND CONSTRAINTS (18. ...Details: THE FINAL REFINED STRUCTURES ARE BASED ON A TOTAL OF 1402 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 153 DIHEDRAL ANGLE CONSTRAINTS, AND 56 HYDROGEN BOND CONSTRAINTS (18.3 CONSTRAINTS PER RESIDUE, 7.0 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 91 BY PSVS 1.4). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA 3.0. THE 20 STRUCTURES OUT OF 100 WITH THE LOWEST TARGET FUNCTION WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS 1.3) WITH PARAM19. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 1402 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 |