6QXN | pdb_00006qxn

Crystal structure of the CCA-adding enzyme of a psychrophilic organism in complex with CTP

PDB DOI: https://doi.org/10.2210/pdb6QXN/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Planococcus halocryophilus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-03-07 Released: 2020-03-25
Deposition Author(s): de Wijn, R., Rollet, K., Bluhm, A., Hennig, O., Betat, H., Moerl, M., Lorber, B., Sauter, C.
Funding Organization(s): French National Research Agency, French Infrastructure for Integrated Structural Biology

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.219 (Depositor), 0.222 (DCC)
R-Value Work:
0.202 (Depositor), 0.206 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

CCA-addition in the cold: Structural characterization of the psychrophilic CCA-adding enzyme from the permafrost bacterium Planococcus halocryophilus

de Wijn, R., Rollet, K., Ernst, F.G., Wellner, K., Betat, H., Morl, M., Sauter, C.

(2021) Comput Struct Biotechnol J

DOI: https://doi.org/10.1016/j.csbj.2021.10.018

Macromolecule Content

Total Structure Weight: 49.44 kDa
Atom Count: 3,398
Modeled Residue Count: 376
Deposited Residue Count: 420
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CCA-adding enzyme	A	420	Planococcus halocryophilus	Mutation(s): 0 Gene Names: BBI08_05760 EC: 2.7.7.72
UniProt
Find proteins for A0A1C7DQ98 (Planococcus halocryophilus) Explore A0A1C7DQ98 Go to UniProtKB: A0A1C7DQ98
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1C7DQ98
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CTP Query on CTP 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]	CYTIDINE-5'-TRIPHOSPHATE C₉ H₁₆ N₃ O₁₄ P₃ PCDQPRRSZKQHHS-XVFCMESISA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	E [auth A], F [auth A], G [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]