6F2F | pdb_00006f2f

Crystal structure of Protease 1 from Pyrococcus Horikoshii co-cystallized in presence of 10 mM Tb-Xo4 and ammonium sulfate.

PDB DOI: https://doi.org/10.2210/pdb6F2F/pdb

Classification: CELL CYCLE
Organism(s): Pyrococcus horikoshii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-11-24 Released: 2018-10-03
Deposition Author(s): Engilberge, S., Riobe, F., Di Pietro, S., Franzetti, B., Girard, E., Dumont, E., Maury, O.
Funding Organization(s): French National Research Agency

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.170 (Depositor), 0.154 (DCC)
R-Value Work:
0.161 (Depositor), 0.149 (DCC)
R-Value Observed:
0.161 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Unveiling the Binding Modes of the Crystallophore, a Terbium-based Nucleating and Phasing Molecular Agent for Protein Crystallography.

Engilberge, S., Riobe, F., Wagner, T., Di Pietro, S., Breyton, C., Franzetti, B., Shima, S., Girard, E., Dumont, E., Maury, O.

(2018) Chemistry 24: 9739-9746

PubMed: 29806881 Search on PubMed
DOI: https://doi.org/10.1002/chem.201802172
Primary Citation Related Structures:
6F2F, 6F2H, 6F2I, 6F2J, 6F2K, 6F2M, 6FRM, 6FRN, 6FRO, 6FRQ

PubMed Abstract:
Crystallophores are lanthanide complexes that act as powerful auxiliary for protein crystallography due to their strong nucleating and phasing effects. To get first insights on the mechanisms behind nucleation induced by Crystallophore, we systematically identified various elaborated networks of supramolecular interactions between Tb-Xo4 and subset of 6 protein structures determined by X-ray diffraction in complex with terbium-Crystallophore (Tb-Xo4). Such interaction mapping analyses demonstrate the versatile binding behavior of the Crystallophore and pave the way to a better understanding of its unique properties.

Organizational Affiliation

Univ Grenoble Alpes, CEA, CNRS, IBS, 38000, Grenoble, France.

Macromolecule Content

Total Structure Weight: 58.64 kDa
Atom Count: 4,731
Modeled Residue Count: 498
Deposited Residue Count: 498
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deglycase PH1704	A, B, C	166	Pyrococcus horikoshii	Mutation(s): 0 Gene Names: PH1704 EC: 3.5.1.124 (PDB Primary Data), 3.4.22 (PDB Primary Data)
UniProt
Find proteins for O59413 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O59413 Go to UniProtKB: O59413
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O59413
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7MT Query on 7MT Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain L [auth C] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain L [auth C] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain L [auth C] mmCIF format, chain H [auth B]	D [auth A], H [auth B], L [auth C]	Tb-Xo4 C₂₀ H₂₃ N₅ O₄ Tb JWLMJALAUZUFRC-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain H [auth B] Focus chain L [auth C] Interactions & Density Focus chain D [auth A] Focus chain H [auth B] Focus chain L [auth C]
TB Query on TB Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	TERBIUM(III) ION Tb HKCRVXUAKWXBLE-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain M [auth C] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain M [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain M [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] I [auth B] J [auth B] K [auth B] E [auth A], F [auth A], I [auth B], J [auth B], K [auth B], M [auth C], N [auth C], O [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C]
2HA Query on 2HA Download:Ideal Coordinates CCD File SDF format, chain P [auth C] MOL2 format, chain P [auth C] mmCIF format, chain P [auth C]	P [auth C]	Dihydroxyacetone C₃ H₆ O₃ RXKJFZQQPQGTFL-UHFFFAOYSA-N		Interactions Focus chain P [auth C] Interactions & Density Focus chain P [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.170 (Depositor), 0.154 (DCC)
R-Value Work: 0.161 (Depositor), 0.149 (DCC)
R-Value Observed: 0.161 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.588	α = 90
b = 124.588	β = 90
c = 128.866	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-10-03

Deposition Author(s):

Funding Organization	Location	Grant Number
French National Research Agency	France	ANR-13-BS07-0007-01

Revision History (Full details and data files)

Version 1.0: 2018-10-03
Type: Initial release
Version 1.1: 2019-05-29
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2019-10-16
Changes: Data collection
Version 1.3: 2020-07-08
Changes: Derived calculations, Structure summary
Version 1.4: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description