PDB-8s2v: SSX structure of Lysozyme grown in microfluidic droplets

ID or keywords:

Entry

Database: PDB / ID: 8s2v

Title

SSX structure of Lysozyme grown in microfluidic droplets

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	8s2v.cif.gz	44.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8s2v.ent.gz	27.8 KB	Display	PDB format
PDBx/mmJSON format	8s2v.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8s2v_validation.pdf.gz	393 KB	Display	wwPDB validaton report
Full document	8s2v_full_validation.pdf.gz	392.9 KB	Display
Data in XML	8s2v_validation.xml.gz	7.4 KB	Display
Data in CIF	8s2v_validation.cif.gz	9.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s2/8s2v ftp://data.pdbj.org/pub/pdb/validation_reports/s2/8s2v	HTTPS FTP

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Related structure data

Related structure data	8s2uC 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

14.4 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)	78.9, 78.9, 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-336- HOH

#1: Protein	Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV Mass: 14331.160 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.: 66 / 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: 40.23 %
Crystal grow	Temperature: 294 K / Method: microfluidic / pH: 3 Details: 20 mg/mL Lysozyme dissolved in 20 mM sodium acetate pH 4.6 Precipitant: 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→78.9 Å / Num. obs: 11607 / % possible obs: 100 % / Redundancy: 464 % / B_iso Wilson estimate: 24.06 Å² / CC_1/2: 0.99 / CC star: 0.99 / Net I/σ(I): 17.2
Reflection shell	Resolution: 1.8→1.83 Å / Redundancy: 51.94 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 663 / CC_1/2: 0.44 / CC star: 0.78 / % possible all: 100
Serial crystallography sample delivery	Description: SOS Chip / Method: fixed target
Serial crystallography data reduction	Crystal hits: 22815 / Frames indexed: 22304 / 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→55.853 Å / Cor.coef. F_o:F_c: 0.978 / Cor.coef. F_o:F_c free: 0.967 / WR_factor R_free: 0.185 / WR_factor R_work: 0.136 / SU B: 2.801 / SU ML: 0.081 / Average fsc free: 0.9647 / Average fsc work: 0.9773 / Cross valid method: FREE R-VALUE / ESU R: 0.112 / ESU R Free: 0.111
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1897	581	5.023 %
R_work	0.1456	10986	-
all	0.148	-	-
obs	-	11567	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: 32.594 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.001 Å²	-0 Å²	0 Å²
2-	-	0.001 Å²	-0 Å²
3-	-	-	-0.002 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→55.853 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1001	0	2	66	1069

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	1095
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	1014
X-RAY DIFFRACTION	r_angle_refined_deg	1.767	1.787	1491
X-RAY DIFFRACTION	r_angle_other_deg	0.601	1.812	2303
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.733	5	141
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	5.959	5	14
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.028	10	182
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.988	10	56
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	151
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	1445
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	311
X-RAY DIFFRACTION	r_nbd_refined	0.239	0.2	229
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.212	0.2	889
X-RAY DIFFRACTION	r_nbtor_refined	0.205	0.2	547
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	571
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.181	0.2	52
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.043	0.2	2
X-RAY DIFFRACTION	r_nbd_other	0.153	0.2	27
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.138	0.2	10
X-RAY DIFFRACTION	r_mcbond_it	2.497	2.856	547
X-RAY DIFFRACTION	r_mcbond_other	2.427	2.856	547
X-RAY DIFFRACTION	r_mcangle_it	3.149	5.117	692
X-RAY DIFFRACTION	r_mcangle_other	3.185	5.125	693
X-RAY DIFFRACTION	r_scbond_it	4.351	3.418	548
X-RAY DIFFRACTION	r_scbond_other	4.348	3.42	549
X-RAY DIFFRACTION	r_scangle_it	6.812	6.019	798
X-RAY DIFFRACTION	r_scangle_other	6.807	6.021	799
X-RAY DIFFRACTION	r_lrange_it	7.614	27.898	1282
X-RAY DIFFRACTION	r_lrange_other	7.613	27.463	1273

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	0.341	40	0.331	777	0.331	817	0.885	0.918	100	0.329
1.847-1.897	0.259	50	0.27	778	0.269	828	0.941	0.947	100	0.257
1.897-1.952	0.236	41	0.239	735	0.239	776	0.962	0.962	100	0.224
1.952-2.012	0.194	35	0.197	740	0.197	775	0.976	0.974	100	0.169
2.012-2.078	0.193	32	0.16	721	0.162	753	0.98	0.982	100	0.138
2.078-2.151	0.241	39	0.147	677	0.152	716	0.962	0.986	100	0.127
2.151-2.232	0.194	35	0.15	686	0.152	721	0.978	0.987	100	0.13
2.232-2.323	0.212	37	0.136	631	0.14	668	0.97	0.988	100	0.117
2.323-2.426	0.195	37	0.137	606	0.14	643	0.977	0.989	100	0.121
2.426-2.544	0.151	27	0.134	613	0.134	640	0.982	0.989	100	0.117
2.544-2.682	0.159	36	0.134	548	0.136	584	0.984	0.989	100	0.119
2.682-2.844	0.202	23	0.136	541	0.138	564	0.972	0.989	100	0.123
2.844-3.04	0.213	25	0.144	520	0.148	545	0.975	0.986	100	0.135
3.04-3.282	0.178	21	0.141	479	0.143	500	0.984	0.988	100	0.139
3.282-3.594	0.193	24	0.143	437	0.146	461	0.98	0.989	100	0.146
3.594-4.017	0.202	24	0.123	405	0.127	429	0.984	0.991	100	0.133
4.017-4.634	0.165	15	0.097	371	0.099	386	0.983	0.994	100	0.109
4.634-5.666	0.1	20	0.13	307	0.128	328	0.993	0.991	99.6951	0.151
5.666-7.972	0.193	16	0.167	252	0.169	268	0.986	0.984	100	0.19
7.972-55.853	0.437	4	0.15	163	0.152	167	0.623	0.983	100	0.189

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