6F2H | pdb_00006f2h

Structure of Protease 1 from Pyrococcus horikoshii co-crystallized in presence of 10 mM Tb-Xo4 and potassium iodide.

PDB DOI: https://doi.org/10.2210/pdb6F2H/pdb

Classification: HYDROLASE
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: 2.19 Å
R-Value Free:
0.193 (Depositor), 0.194 (DCC)
R-Value Work:
0.150 (Depositor), 0.151 (DCC)
R-Value Observed:
0.152 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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: 231.64 kDa
Atom Count: 16,798
Modeled Residue Count: 1,992
Deposited Residue Count: 1,992
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, D, E A, B, C, D, E, F, G, H, I, J, K, L	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7MT Query on 7MT Download:Ideal Coordinates CCD File SDF format, chain FA [auth I] SDF format, chain IA [auth J] SDF format, chain LA [auth K] SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain V [auth E] SDF format, chain Z [auth F] SDF format, chain NA [auth L] SDF format, chain BA [auth G] MOL2 format, chain FA [auth I] MOL2 format, chain IA [auth J] MOL2 format, chain LA [auth K] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain V [auth E] MOL2 format, chain Z [auth F] MOL2 format, chain NA [auth L] MOL2 format, chain BA [auth G] mmCIF format, chain FA [auth I] mmCIF format, chain IA [auth J] mmCIF format, chain LA [auth K] mmCIF format, chain M [auth A] mmCIF format, chain O [auth B] mmCIF format, chain V [auth E] mmCIF format, chain Z [auth F] mmCIF format, chain NA [auth L] mmCIF format, chain BA [auth G]	BA [auth G] FA [auth I] IA [auth J] LA [auth K] M [auth A] BA [auth G], FA [auth I], IA [auth J], LA [auth K], M [auth A], NA [auth L], O [auth B], V [auth E], Z [auth F]	Tb-Xo4 C₂₀ H₂₃ N₅ O₄ Tb JWLMJALAUZUFRC-UHFFFAOYSA-L		Interactions Focus chain BA [auth G] Focus chain FA [auth I] Focus chain IA [auth J] Focus chain LA [auth K] Focus chain M [auth A] Focus chain NA [auth L] Focus chain O [auth B] Focus chain V [auth E] Focus chain Z [auth F] Interactions & Density Focus chain BA [auth G] Focus chain FA [auth I] Focus chain IA [auth J] Focus chain LA [auth K] Focus chain M [auth A] Focus chain NA [auth L] Focus chain O [auth B] Focus chain V [auth E] Focus chain Z [auth F]
TB Query on TB Download:Ideal Coordinates CCD File SDF format, chain DA [auth H] SDF format, chain HA [auth J] SDF format, chain S [auth D] SDF format, chain T [auth E] SDF format, chain U [auth E] SDF format, chain X [auth F] SDF format, chain Y [auth F] SDF format, chain Q [auth C] SDF format, chain KA [auth K] MOL2 format, chain DA [auth H] MOL2 format, chain HA [auth J] MOL2 format, chain S [auth D] MOL2 format, chain T [auth E] MOL2 format, chain U [auth E] MOL2 format, chain X [auth F] MOL2 format, chain Y [auth F] MOL2 format, chain Q [auth C] MOL2 format, chain KA [auth K] mmCIF format, chain DA [auth H] mmCIF format, chain HA [auth J] mmCIF format, chain S [auth D] mmCIF format, chain T [auth E] mmCIF format, chain U [auth E] mmCIF format, chain X [auth F] mmCIF format, chain Y [auth F] mmCIF format, chain Q [auth C] mmCIF format, chain KA [auth K]	DA [auth H] HA [auth J] KA [auth K] Q [auth C] S [auth D] DA [auth H], HA [auth J], KA [auth K], Q [auth C], S [auth D], T [auth E], U [auth E], X [auth F], Y [auth F]	TERBIUM(III) ION Tb HKCRVXUAKWXBLE-UHFFFAOYSA-N		Interactions Focus chain DA [auth H] Focus chain HA [auth J] Focus chain KA [auth K] Focus chain Q [auth C] Focus chain S [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain X [auth F] Focus chain Y [auth F] Interactions & Density Focus chain DA [auth H] Focus chain HA [auth J] Focus chain KA [auth K] Focus chain Q [auth C] Focus chain S [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain X [auth F] Focus chain Y [auth F]
IOD Query on IOD Download:Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain GA [auth I] SDF format, chain JA [auth J] SDF format, chain N [auth A] SDF format, chain OA [auth L] SDF format, chain P [auth B] SDF format, chain W [auth E] SDF format, chain R [auth C] SDF format, chain MA [auth K] SDF format, chain EA [auth H] SDF format, chain CA [auth G] MOL2 format, chain AA [auth F] MOL2 format, chain GA [auth I] MOL2 format, chain JA [auth J] MOL2 format, chain N [auth A] MOL2 format, chain OA [auth L] MOL2 format, chain P [auth B] MOL2 format, chain W [auth E] MOL2 format, chain R [auth C] MOL2 format, chain MA [auth K] MOL2 format, chain EA [auth H] MOL2 format, chain CA [auth G] mmCIF format, chain AA [auth F] mmCIF format, chain GA [auth I] mmCIF format, chain JA [auth J] mmCIF format, chain N [auth A] mmCIF format, chain OA [auth L] mmCIF format, chain P [auth B] mmCIF format, chain W [auth E] mmCIF format, chain R [auth C] mmCIF format, chain MA [auth K] mmCIF format, chain EA [auth H] mmCIF format, chain CA [auth G]	AA [auth F] CA [auth G] EA [auth H] GA [auth I] JA [auth J] AA [auth F], CA [auth G], EA [auth H], GA [auth I], JA [auth J], MA [auth K], N [auth A], OA [auth L], P [auth B], R [auth C], W [auth E]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain AA [auth F] Focus chain CA [auth G] Focus chain EA [auth H] Focus chain GA [auth I] Focus chain JA [auth J] Focus chain MA [auth K] Focus chain N [auth A] Focus chain OA [auth L] Focus chain P [auth B] Focus chain R [auth C] Focus chain W [auth E] Interactions & Density Focus chain AA [auth F] Focus chain CA [auth G] Focus chain EA [auth H] Focus chain GA [auth I] Focus chain JA [auth J] Focus chain MA [auth K] Focus chain N [auth A] Focus chain OA [auth L] Focus chain P [auth B] Focus chain R [auth C] Focus chain W [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.193 (Depositor), 0.194 (DCC)
R-Value Work: 0.150 (Depositor), 0.151 (DCC)
R-Value Observed: 0.152 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.577	α = 90
b = 84.698	β = 90.97
c = 144.343	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
autoSHARP	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: 2024-05-08
Changes: Data collection, Database references, Derived calculations