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Yorodumi- PDB-2k5d: SOLUTION NMR STRUCTURE OF SAG0934 from Streptococcus agalactiae. ... -
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-Basic information
Entry | Database: PDB / ID: 2k5d | ||||||
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Title | SOLUTION NMR STRUCTURE OF SAG0934 from Streptococcus agalactiae. NORTHEAST STRUCTURAL GENOMICS TARGET SaR32[1-108]. | ||||||
Components | uncharacterized protein SAG0934 | ||||||
Keywords | structural genomics / unknown function / solution NMR structure / primosomal protein / DUF961 / construct optimized / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Conjugative transposon protein, DUF961 / Protein of unknown function DUF961 / YdcP-like superfamily / Bacterial protein of unknown function (DUF961) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta / Uncharacterized protein Function and homology information | ||||||
Biological species | Streptococcus agalactiae serogroup V (bacteria) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Aramini, J.M. / Rossi, P. / Zhao, L. / Foote, E.L. / Jiang, M. / Xiao, R. / Sharma, S. / Swapna, G.VT. / Nair, R. / Everett, J.K. ...Aramini, J.M. / Rossi, P. / Zhao, L. / Foote, E.L. / Jiang, M. / Xiao, R. / Sharma, S. / Swapna, G.VT. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: SOLUTION NMR STRUCTURE OF SAG0934 from Streptococcus agalactiae. NORTHEAST STRUCTURAL GENOMICS TARGET SaR32[1-108]. Authors: Aramini, J.M. / Rossi, P. / Zhao, L. / Foote, E.L. / Jiang, M. / Xiao, R. / Sharma, S. / Swapna, G.VT. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. / 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 | 2k5d.cif.gz | 781.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2k5d.ent.gz | 660.8 KB | Display | PDB format |
PDBx/mmJSON format | 2k5d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2k5d_validation.pdf.gz | 543.1 KB | Display | wwPDB validaton report |
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Full document | 2k5d_full_validation.pdf.gz | 703.2 KB | Display | |
Data in XML | 2k5d_validation.xml.gz | 43.1 KB | Display | |
Data in CIF | 2k5d_validation.cif.gz | 62.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k5/2k5d ftp://data.pdbj.org/pub/pdb/validation_reports/k5/2k5d | HTTPS FTP |
-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: 13225.892 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus agalactiae serogroup V (bacteria) Species: agalactiae / Description: pET21 vector / Gene: SAG0934 / Species (production host): coli / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MGK / References: UniProt: Q8E006 |
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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, STATIC LIGHT SCATTERING AND 15N T1/T2 RELAXATION. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED ...Text: THE PROTEIN IS MONOMERIC BY GEL FILTRATION CHROMATOGRAPHY, STATIC LIGHT SCATTERING AND 15N T1/T2 RELAXATION. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN, AND THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS WERE DETERMINED USING CYANA 2.1. BACKBONE (PHI/PSI) DIHEDRAL ANGLE CONSTRAINTS WERE OBTAINED FROM TALOS. HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING BOTH AUTOSTRUCTURE AND CYANA, AND WERE APPLIED ONLY IN THE FINAL REFINEMENT STAGE (CNS) OF THE STRUCTURE DETERMINATION. ROTAMER STATES OF SPECIFIC ORDERED RESIDUES WERE CONSTRAINED IN THE FINAL STAGE OF THE STRUCTURE REFINEMENT BASED ON PROCHECK. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C-TERMINAL HHHHHH): BACKBONE, 99.5%, SIDE CHAIN, 97.2%, AROMATICS, 100%, STEREOSPECIFIC METHYL, 94.4%, STEREOSPECIFIC SIDE CHAIN NH2: 100%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 1 TO 110, PSVS 1.3), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 18-50,53-67,70-72,74-78,81-83,99-108: (A) RMSD (ORDERED RESIDUES): BB, 0.7, HEAVY ATOM, 1.0. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 90.5%, ADDITIONALLY ALLOWED, 9.5%, GENEROUSLY ALLOWED, 0.0%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.55/-1.85, ALL, -0.28/-1.66. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 17.32/-1.45 (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 1-110): RECALL, 0.989, PRECISION, 0.916, F-MEASURE, 0.951, DP-SCORE, 0.751. (F) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 15. THE C-TERMINAL HIS TAG RESIDUES OF THE PROTEIN (HHHHHH) 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]: 1-17,51-52,68-69,73,84-98,109-110. |
-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 0.1 / 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 STRUCTURES ARE BASED ON A TOTAL OF 1629 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 100 DIHEDRAL ANGLE CONSTRAINTS, AND 38 HYDROGEN BOND CONSTRAINTS (16.2 ...Details: THE FINAL STRUCTURES ARE BASED ON A TOTAL OF 1629 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 100 DIHEDRAL ANGLE CONSTRAINTS, AND 38 HYDROGEN BOND CONSTRAINTS (16.2 CONSTRAINTS PER RESIDUE, 5.0 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 110 BY PSVS 1.3). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA 2.1. THE 20 STRUCTURES OUT OF 100 WITH THE LOWEST TARGET FUNCTION WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) WITH PARAM19. | ||||||||||||||||||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 1629 / NOE intraresidue total count: 514 / NOE long range total count: 509 / NOE medium range total count: 137 / NOE sequential total count: 469 / Hydrogen bond constraints total count: 38 / Protein chi angle constraints total count: 13 / Protein other angle constraints total count: 13 / Protein phi angle constraints total count: 38 / Protein psi angle constraints total count: 38 | ||||||||||||||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Average torsion angle constraint violation: 0.49 ° Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 4 ° / Maximum upper distance constraint violation: 0.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.01 Å |