6TVY | pdb_00006tvy

Structure of hen egg white lysozyme crystallized in the presence of Tb-Xo4 crystallophore in the XtalController device

PDB DOI: https://doi.org/10.2210/pdb6TVY/pdb

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

Deposited: 2020-01-10 Released: 2020-12-16
Deposition Author(s): de Wijn, R., Rollet, K., Coudray, L., McEwen, A.G., Lorber, B., Sauter, C.
Funding Organization(s): French National Research Agency, French Infrastructure for Integrated Structural Biology (FRISBI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.51 Å
R-Value Free:
0.175 (Depositor), 0.175 (DCC)
R-Value Work:
0.141 (Depositor), 0.142 (DCC)
R-Value Observed:
0.145 (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

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: 15.3 kDa
Atom Count: 1,090
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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7MT (Subject of Investigation/LOI) Query on 7MT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	Tb-Xo4 C₂₀ H₂₃ N₅ O₄ Tb JWLMJALAUZUFRC-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
TB Query on TB Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A]	TERBIUM(III) ION Tb HKCRVXUAKWXBLE-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
NA Query on NA 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]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.51 Å
R-Value Free: 0.175 (Depositor), 0.175 (DCC)
R-Value Work: 0.141 (Depositor), 0.142 (DCC)
R-Value Observed: 0.145 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.81	α = 90
b = 78.81	β = 90
c = 38.332	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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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
French National Research Agency	France	ANR-13-BS07-0007-01
French Infrastructure for Integrated Structural Biology (FRISBI)	France	ANR-10-INSB-05

Revision History (Full details and data files)

Version 1.0: 2020-12-16
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary