5FST

Structure of lysozyme prepared by the 'soak-and-freeze' method under 100 bar of krypton pressure

PDB DOI: https://doi.org/10.2210/pdb5FST/pdb

Classification: HYDROLASE
Organism(s): Gallus gallus
Mutation(s): No

Deposited: 2016-01-07 Released: 2016-10-26
Deposition Author(s): Lafumat, B., Mueller-Dieckmann, C., Colloc'h, N., Prange, T., Royant, A., van der Linden, P., Carpentier, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.134
R-Value Work: 0.109
R-Value Observed: 0.110

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Gas-Sensitive Biological Crystals Processed in Pressurized Oxygen and Krypton Atmospheres: Deciphering Gas Channels in Proteins Using a Novel `Soak-and-Freeze' Methodology.

Lafumat, B., Mueller-Dieckmann, C., Colloc'h, N., Prange, T., Royant, A., van der Linden, P., Carpentier, P.

(2016) J Appl Crystallogr 49: 1478

DOI: https://doi.org/10.1107/S1600576716010992

Macromolecule Content

Total Structure Weight: 15.06 kDa
Atom Count: 1,300
Modelled Residue Count: 129
Deposited Residue Count: 129
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00698
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KR Query on KR Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain L [auth A]	K [auth A], L [auth A], M [auth A], N [auth A], O [auth A]	KRYPTON Kr DNNSSWSSYDEUBZ-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [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 E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.134
R-Value Work: 0.109
R-Value Observed: 0.110
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.001	α = 90
b = 79.001	β = 90
c = 37.053	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2016-10-26

Deposition Author(s):

Lafumat, B.

Mueller-Dieckmann, C.

Revision History (Full details and data files)

Version 1.0: 2016-10-26
Type: Initial release
Version 1.1: 2016-11-16
Changes: Structure summary
Version 1.2: 2017-05-10
Changes: Structure summary
Version 1.3: 2018-02-21
Changes: Database references, Structure summary
Version 1.4: 2019-07-17
Changes: Data collection, Derived calculations
Version 1.5: 2024-01-10
Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.6: 2024-11-06
Changes: Structure summary