9GHX | pdb_00009ghx

Lysozyme covalently bound to fac-[Re(CO)3-imidazole] complex, incubated for 112 weeks. Data collection done at mammalian body temperature.

PDB DOI: https://doi.org/10.2210/pdb9GHX/pdb

Classification: ANTIMICROBIAL PROTEIN
Organism(s): Gallus gallus
Mutation(s): No

Deposited: 2024-08-16 Released: 2024-10-16
Deposition Author(s): Jacobs, F.J.F., Brink, A., Helliwell, J.R.
Funding Organization(s): National Research Foundation in South Africa, Other government, Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free:
0.271 (Depositor), 0.269 (DCC)
R-Value Work:
0.204 (Depositor)
R-Value Observed:
0.211 (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

Body temperature protein X-ray crystallography at 37 °C: a rhenium protein complex seeking a physiological condition structure.

Jacobs, F.J.F., Helliwell, J.R., Brink, A.

(2024) Chem Commun (Camb) 60: 14030-14033

PubMed: 39382205 Search on PubMed
DOI: https://doi.org/10.1039/d4cc04245j
Primary Citation Related Structures:
9GHX

PubMed Abstract:
The retention of the covalent binding of an organometalllic rhenium complex as a model for a technetium-99m imaging agent, to a protein at physiological body temperature 37 °C is described. Detailed structure comparisons are made to the related 100 K crystal structure. The generality of the need for this sort of analytical procedure for guiding ligand lead compound discovery is emphasised.

Organizational Affiliation

Department of Chemistry, University of the Free State, Nelson Mandela Drive, Bloemfontein 9301, South Africa.

Macromolecule Content

Total Structure Weight: 16.1 kDa
Atom Count: 1,087
Modeled Residue Count: 129
Deposited Residue Count: 129
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	129	Gallus gallus	Mutation(s): 0 EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698 Go to UniProtKB: P00698
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00698
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VHL Query on VHL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A]	Tricarbonyl di(imidazole) rhenium(I) C₉ H₆ N₄ O₃ Re MWUHNOZKPZGOSW-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
REI Query on REI 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]	Tricarbonyl (aqua) (imidazole) rhenium(I) C₆ H₆ N₂ O₄ Re KPOHHEXTCRHHSE-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
RE Query on RE Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	J [auth A], K [auth A]	RHENIUM Re WUAPFZMCVAUBPE-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A]
IMD Query on IMD 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]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain L [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain L [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A], L [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain L [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain L [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.271 (Depositor), 0.269 (DCC)
R-Value Work: 0.204 (Depositor)
R-Value Observed: 0.211 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.493	α = 90
b = 81.493	β = 90
c = 37.413	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
APEX	data reduction
APEX	data collection
Aimless	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: 2024-10-16

Deposition Author(s):

Jacobs, F.J.F.

Brink, A.

Helliwell, J.R.

Funding Organization	Location	Grant Number
National Research Foundation in South Africa	South Africa	--
Other government		DHET Future Professors Program
Other private		SASOL University Collaboration Initiative