PDB-8s2u: SSX structure of Lysozyme grown in batch conditions

ID or keywords:

Entry

Database: PDB / ID: 8s2u

Title

SSX structure of Lysozyme grown in batch conditions

Components

Lysozyme C

Keywords

HYDROLASE

Function / homology

Function and homology information

Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...
Similarity search - Function

Biological species

Gallus gallus (chicken)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Stubbs, J. / Tews, I. / Maly, M.

Funding support

United Kingdom, 2items

Organization	Grant number	Country
Biotechnology and Biological Sciences Research Council (BBSRC)	BB/S008470/1	United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)	BB/T008768/1	United Kingdom

Citation

Journal: Iucrj / Year: 2024
Title: Droplet microfluidics for time-resolved serial crystallography.
Authors: Stubbs, J. / Hornsey, T. / Hanrahan, N. / Esteban, L.B. / Bolton, R. / Maly, M. / Basu, S. / Orlans, J. / de Sanctis, D. / Shim, J.U. / Shaw Stewart, P.D. / Orville, A.M. / Tews, I. / West, J.

History

Deposition	Feb 19, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 28, 2024	Provider: repository / Type: Initial release
Revision 1.1	Mar 20, 2024	Group: Database references / Category: citation / citation_author
Revision 1.2	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8s2u.cif.gz	44.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8s2u.ent.gz	27.5 KB	Display	PDB format
PDBx/mmJSON format	8s2u.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8s2u_validation.pdf.gz	400.8 KB	Display	wwPDB validaton report
Full document	8s2u_full_validation.pdf.gz	400.8 KB	Display
Data in XML	8s2u_validation.xml.gz	7.3 KB	Display
Data in CIF	8s2u_validation.cif.gz	9.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s2/8s2u ftp://data.pdbj.org/pub/pdb/validation_reports/s2/8s2u	HTTPS FTP

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Related structure data

Related structure data	8s2vC 8s2wC 8s2xC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (3) #136 - Apr 2011 Nanobodies similarity (3) #222 - Jun 2018 Proteins and Nanoparticles similarity (3) #9 - Sep 2000 Lysozyme similarity (3) #142 - Oct 2011 PDB Pioneers similarity (3)

Deposited unit

A: Lysozyme C

hetero molecules

16.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	79, 79, 37.9
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	96
Space group name H-M	P4₃2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-333- HOH
2	1	A-358- HOH

#1: Protein	Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV Mass: 16257.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.06 Å³/Da / Density % sol: 40.38 %
Crystal grow	Temperature: 294 K / Method: batch mode / pH: 3 Details: Protein dissolved in 20 mM sodium acetate pH 4.6 Protein and precipitant mixed in a 1:4 ratio Precipitant solution: 6% PEG 6000 (w/v), 3.4M NaCl and 1M sodium acetate pH 3.0

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Data collection

Diffraction	Mean temperature: 293 K / Serial crystal experiment: Y
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07 Å
Detector	Type: PSI JUNGFRAU 4M / Detector: PIXEL / Date: Jan 23, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.07 Å / Relative weight: 1
Reflection	Resolution: 1.8→79 Å / Num. obs: 11636 / % possible obs: 100 % / Redundancy: 438 % / B_iso Wilson estimate: 30.46 Å² / CC_1/2: 0.99 / CC star: 0.99 / Net I/σ(I): 13.5
Reflection shell	Resolution: 1.8→1.83 Å / Redundancy: 47.67 % / Mean I/σ(I) obs: 0.2 / Num. unique obs: 669 / CC_1/2: 0.49 / CC star: 0.81 / % possible all: 100
Serial crystallography sample delivery	Description: SOS Chip / Method: fixed target
Serial crystallography data reduction	Crystal hits: 34032 / Frames indexed: 29954 / Frames total: 81800

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
CrystFEL	0.10.2	data reduction
CrystFEL	0.10.2	data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.8→55.924 Å / Cor.coef. F_o:F_c: 0.975 / Cor.coef. F_o:F_c free: 0.955 / WR_factor R_free: 0.208 / WR_factor R_work: 0.148 / SU B: 3.927 / SU ML: 0.108 / Average fsc free: 0.9331 / Average fsc work: 0.9534 / Cross valid method: FREE R-VALUE / ESU R: 0.126 / ESU R Free: 0.133
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2307	581	5.01 %
R_work	0.1706	11016	-
all	0.173	-	-
obs	-	11597	99.991 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 38.199 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.004 Å²	0 Å²	-0 Å²
2-	-	-0.004 Å²	0 Å²
3-	-	-	0.008 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→55.924 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1001	0	2	59	1062

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	1050
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	967
X-RAY DIFFRACTION	r_angle_refined_deg	1.551	1.778	1426
X-RAY DIFFRACTION	r_angle_other_deg	0.562	1.8	2201
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.997	5	133
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.961	5	11
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.871	10	172
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.297	10	52
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	147
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	1352
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	288
X-RAY DIFFRACTION	r_nbd_refined	0.222	0.2	225
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.202	0.2	868
X-RAY DIFFRACTION	r_nbtor_refined	0.181	0.2	546
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	562
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.175	0.2	32
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.091	0.2	6
X-RAY DIFFRACTION	r_nbd_other	0.118	0.2	35
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.105	0.2	11
X-RAY DIFFRACTION	r_mcbond_it	2.719	3.403	527
X-RAY DIFFRACTION	r_mcbond_other	2.721	3.401	527
X-RAY DIFFRACTION	r_mcangle_it	3.43	6.092	660
X-RAY DIFFRACTION	r_mcangle_other	3.453	6.1	661
X-RAY DIFFRACTION	r_scbond_it	4.325	4	523
X-RAY DIFFRACTION	r_scbond_other	4.321	4.004	524
X-RAY DIFFRACTION	r_scangle_it	6.642	7.085	765
X-RAY DIFFRACTION	r_scangle_other	6.638	7.089	766
X-RAY DIFFRACTION	r_lrange_it	8.004	33.734	1237
X-RAY DIFFRACTION	r_lrange_other	7.97	33.543	1232

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.8-1.847	0.478	40	0.415	788	0.418	828	0.731	0.85	100	0.411
1.847-1.897	0.417	50	0.392	777	0.393	827	0.839	0.869	100	0.393
1.897-1.952	0.315	41	0.373	735	0.37	776	0.922	0.888	100	0.372
1.952-2.012	0.293	35	0.3	741	0.299	776	0.93	0.927	100	0.293
2.012-2.078	0.26	32	0.258	723	0.258	755	0.948	0.95	100	0.239
2.078-2.151	0.3	39	0.204	686	0.208	725	0.937	0.969	100	0.179
2.151-2.232	0.223	35	0.191	679	0.193	714	0.971	0.976	100	0.166
2.232-2.323	0.229	37	0.158	634	0.162	671	0.957	0.984	100	0.133
2.323-2.426	0.199	37	0.146	609	0.148	646	0.98	0.987	100	0.123
2.426-2.544	0.229	27	0.152	612	0.155	639	0.968	0.984	100	0.128
2.544-2.682	0.196	35	0.151	551	0.153	586	0.981	0.986	100	0.128
2.682-2.844	0.251	24	0.154	541	0.158	565	0.954	0.986	100	0.133
2.844-3.04	0.163	25	0.138	522	0.139	547	0.98	0.988	100	0.121
3.04-3.282	0.161	21	0.142	480	0.142	501	0.983	0.987	100	0.129
3.282-3.595	0.237	24	0.155	439	0.159	463	0.972	0.985	100	0.148
3.595-4.017	0.264	24	0.147	403	0.154	427	0.965	0.986	100	0.147
4.017-4.634	0.237	14	0.114	371	0.117	385	0.97	0.991	100	0.118
4.634-5.666	0.14	21	0.141	310	0.141	331	0.99	0.988	100	0.146
5.666-7.972	0.219	16	0.171	251	0.175	268	0.98	0.982	99.6269	0.181
7.972-55.924	0.582	4	0.177	164	0.181	168	0.769	0.979	100	0.204

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