Discovery of the Universal tRNA Binding Mode for the TsaD-like Components of the t6A tRNA Modification Pathway
Stec, B.(2023) Biophysica 3: 288-306
Experimental Data Snapshot
Starting Model: experimental
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This entry reflects an alternative modeling of the original data in: 6FPE
(2023) Biophysica 3: 288-306
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
tRNA threonylcarbamoyladenosine biosynthesis protein TsaB | A, D [auth C] | 206 | Thermotoga maritima MSB8 | Mutation(s): 0  Gene Names: tsaB, TM_0874, Tmari_0876 | |
UniProt | |||||
Find proteins for Q9WZX7 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WZX7  Go to UniProtKB:  Q9WZX7 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9WZX7 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 2 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
tRNA N6-adenosine threonylcarbamoyltransferase | B, E [auth G] | 327 | Thermotoga maritima MSB8 | Mutation(s): 0  Gene Names: tsaD, gcp, TM_0145 EC: 2.3.1.234 | |
UniProt | |||||
Find proteins for Q9WXZ2 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WXZ2  Go to UniProtKB:  Q9WXZ2 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9WXZ2 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 3 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
TsaE | C [auth D], F [auth E] | 184 | Thermotoga maritima MSB8 | Mutation(s): 0  Gene Names: TsaE | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Ligands 4 Unique | |||||
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ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
APC Query on APC | J [auth D], N [auth E] | DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER C11 H18 N5 O12 P3 CAWZRIXWFRFUQB-IOSLPCCCSA-N | |||
TXA Query on TXA | G [auth B], K [auth G] | threonylcarbamoyladenylate C15 H21 N6 O11 P GHLUPQUHEIJRCU-DWVDDHQFSA-N | |||
ZN Query on ZN | H [auth B], L [auth G] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N | |||
MG Query on MG | I [auth D], M [auth E] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |
Length ( Å ) | Angle ( ˚ ) |
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a = 84.31 | α = 90 |
b = 113.99 | β = 90 |
c = 177.57 | γ = 90 |
Software Name | Purpose |
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REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |