6TVZ | pdb_00006tvz

Structure of a psychrophilic CCA-adding enzyme crystallized in the XtalController device

PDB DOI: https://doi.org/10.2210/pdb6TVZ/pdb

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

Deposited: 2020-01-10 Released: 2020-12-16
Deposition Author(s): de Wijn, R., Rollet, K., Coudray, L., Hennig, O., Betat, H., Moerl, M., Lorber, B., Sauter, C.
Funding Organization(s): French National Research Agency

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free:
0.257 (Depositor), 0.258 (DCC)
R-Value Work:
0.214 (Depositor), 0.218 (DCC)
R-Value Observed:
0.216 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Monitoring the Production of High Diffraction-Quality Crystals of Two Enzymes in Real Time Using In Situ Dynamic Light Scattering

de Wijn, R., Rollet, K., Engilberge, S., McEwen, A.G., Hennig, O., Betat, H., Moerl, M., Riobe, F., Maury, O., Girard, E., Benas, P., Lorber, B., Sauter, C.

(2020) Crystals (Basel)

DOI: https://doi.org/10.3390/cryst10020065

Macromolecule Content

Total Structure Weight: 49.08 kDa
Atom Count: 3,130
Modeled Residue Count: 366
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
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	D [auth A], E [auth A], F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	G [auth A], H [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free: 0.257 (Depositor), 0.258 (DCC)
R-Value Work: 0.214 (Depositor), 0.218 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.53	α = 90
b = 70.53	β = 90
c = 291.48	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-12-16

Deposition Author(s):

Funding Organization	Location	Grant Number
French National Research Agency	France	ANR-10-LABX-0036_NETRNA
French National Research Agency	France	ANR-11-LABX-0057_MITOCROSS
French National Research Agency	France	ANR-10-LABX-0036_INRT