4E1B

Re-refinement of PDB entry 2EQA - SUA5 protein from Sulfolobus tokodaii with bound threonylcarbamoyladenylate

PDB DOI: https://doi.org/10.2210/pdb4E1B/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Sulfurisphaera tokodaii str. 7
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-03-06 Released: 2012-03-14
Deposition Author(s): Parthier, C., Goerlich, S., Jaenecke, F., Breithaupt, C., Braeuer, U., Fandrich, U., Clausnitzer, D., Wehmeier, U.F., Boettcher, C., Scheel, D., Stubbs, M.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.217 (Depositor), 0.216 (DCC)
R-Value Work:
0.183 (Depositor), 0.183 (DCC)
R-Value Observed:
0.186 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 2EQA

Literature

The O-Carbamoyltransferase TobZ Catalyzes an Ancient Enzymatic Reaction.

Parthier, C., Gorlich, S., Jaenecke, F., Breithaupt, C., Brauer, U., Fandrich, U., Clausnitzer, D., Wehmeier, U.F., Bottcher, C., Scheel, D., Stubbs, M.T.

(2012) Angew Chem Int Ed Engl 51: 4046-4052

PubMed: 22383337 Search on PubMed
DOI: https://doi.org/10.1002/anie.201108896
Primary Citation of Related Structures:
3VEN, 3VEO, 3VER, 3VES, 3VET, 3VEW, 3VEX, 3VEZ, 3VF2, 3VF4, 4E1B

Organizational Affiliation

Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle (Saale), Germany.

Macromolecule Content

Total Structure Weight: 39.6 kDa
Atom Count: 2,776
Modelled Residue Count: 330
Deposited Residue Count: 352
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YrdC/Sua5 family protein	A	352	Sulfurisphaera tokodaii str. 7	Mutation(s): 0 Gene Names: STK_15260, SUA5 EC: 2.7.7.87
UniProt
Find proteins for Q970S6 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore Q970S6 Go to UniProtKB: Q970S6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q970S6
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TXA Query on TXA Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	threonylcarbamoyladenylate C₁₅ H₂₁ N₆ O₁₁ P GHLUPQUHEIJRCU-DWVDDHQFSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.217 (Depositor), 0.216 (DCC)
R-Value Work: 0.183 (Depositor), 0.183 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.391	α = 90
b = 120.843	β = 90
c = 67.552	γ = 90

Software Package:

Software Name	Purpose
BSS	data collection
SOLVE	phasing
REFMAC	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-03-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-03-14
Type: Initial release
Version 1.1: 2012-05-02
Changes: Database references
Version 1.2: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary