1tra: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(14 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1tra.jpg|left|200px]]


{{Structure
==RESTRAINED REFINEMENT OF THE MONOCLINIC FORM OF YEAST PHENYLALANINE TRANSFER RNA. TEMPERATURE FACTORS AND DYNAMICS, COORDINATED WATERS, AND BASE-PAIR PROPELLER TWIST ANGLES==
|PDB= 1tra |SIZE=350|CAPTION= <scene name='initialview01'>1tra</scene>, resolution 3.000&Aring;
<StructureSection load='1tra' size='340' side='right'caption='[[1tra]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=MG:MAGNESIUM ION'>MG</scene>
<table><tr><td colspan='2'>[[1tra]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=8tna 8tna], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=7tna 7tna] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2tna 2tna]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TRA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TRA FirstGlance]. <br>
|ACTIVITY=  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3&#8491;</td></tr>
|GENE=  
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=YG:WYBUTOSINE'>YG</scene></td></tr>
}}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1tra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tra OCA], [https://pdbe.org/1tra PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tra RCSB], [https://www.ebi.ac.uk/pdbsum/1tra PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tra ProSAT]</span></td></tr>
</table>


'''RESTRAINED REFINEMENT OF THE MONOCLINIC FORM OF YEAST PHENYLALANINE TRANSFER RNA. TEMPERATURE FACTORS AND DYNAMICS, COORDINATED WATERS, AND BASE-PAIR PROPELLER TWIST ANGLES'''
==See Also==
 
*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
 
__TOC__
==Overview==
</StructureSection>
The structure of yeast phenylalanine transfer RNA in the monoclinic form has been further refined by using the restrained least-squares method of Hendrickson and Konnert. For the 4019 reflections between 10 and 3 A, with magnitudes at least 3 times their standard deviations, the R factor is 16.8%. The variation of the atomic temperature factors along the sequence indicates that the major flexibility regions are the amino acid and anticodon stems. The two strands of the amino acid helix exhibit large differential temperature factors, suggesting partial uncoiling or melting of the helix. In this work, the occupancy of all atoms was also varied. Residues D16 and D17 of the dihydrouridine loop as well as U33 and G37 of the anticodon loop have occupancies around 70%, indicating some local disorder or large-scale mobility at these positions. One hundred fifteen solvent molecules, including five magnesium ions, were found in difference maps. The role of several water molecules is clearly related to the stabilization of the secondary and tertiary interactions. The gold sites, which were not previously discussed, are described and show an energetically favored binding mode similar to that of cobalt and nickel complexes with nucleotides.
[[Category: Large Structures]]
 
[[Category: Saccharomyces cerevisiae]]
==About this Structure==
[[Category: Sundaralingam M]]
1TRA is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Saccharomyces_servazzii Saccharomyces servazzii]. This structure supersedes the now removed PDB entries 8TNA, 7TNA and 2TNA. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TRA OCA].
[[Category: Westhof E]]
 
==Reference==
Restrained refinement of the monoclinic form of yeast phenylalanine transfer RNA. Temperature factors and dynamics, coordinated waters, and base-pair propeller twist angles., Westhof E, Sundaralingam M, Biochemistry. 1986 Aug 26;25(17):4868-78. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/3533142 3533142]
[[Category: Protein complex]]
[[Category: Saccharomyces servazzii]]
[[Category: Sundaralingam, M.]]
[[Category: Westhof, E.]]
[[Category: MG]]
[[Category: loop]]
[[Category: single strand]]
[[Category: t-rna]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:22:17 2008''

Latest revision as of 11:41, 14 February 2024

RESTRAINED REFINEMENT OF THE MONOCLINIC FORM OF YEAST PHENYLALANINE TRANSFER RNA. TEMPERATURE FACTORS AND DYNAMICS, COORDINATED WATERS, AND BASE-PAIR PROPELLER TWIST ANGLESRESTRAINED REFINEMENT OF THE MONOCLINIC FORM OF YEAST PHENYLALANINE TRANSFER RNA. TEMPERATURE FACTORS AND DYNAMICS, COORDINATED WATERS, AND BASE-PAIR PROPELLER TWIST ANGLES

Structural highlights

1tra is a 1 chain structure with sequence from Saccharomyces cerevisiae. This structure supersedes the now removed PDB entries 8tna, 7tna and 2tna. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3Å
Ligands:, , , , , , , , , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

See Also

1tra, resolution 3.00Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=1tra&oldid=4055664"