PDB-8ezx: Lysozyme Anomalous Dataset at 293 K and 7.1 keV

ID or keywords:

Entry

Database: PDB / ID: 8ezx

Title

Lysozyme Anomalous Dataset at 293 K and 7.1 keV

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 /

SAD / Resolution: 1.9 Å

Authors

Doukov, T. / Yabukarski, F. / Herschlag, D.

Funding support

United States,

France, 2items

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Obtaining anomalous and ensemble information from protein crystals from 220 K up to physiological temperatures.
Authors: Doukov, T. / Herschlag, D. / Yabukarski, F.

History

Deposition	Nov 1, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 15, 2023	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	Oct 23, 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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PDBx/mmCIF format	8ezx.cif.gz	87.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8ezx.ent.gz	51.4 KB	Display	PDB format
PDBx/mmJSON format	8ezx.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ez/8ezx ftp://data.pdbj.org/pub/pdb/validation_reports/ez/8ezx	HTTPS FTP

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Related structure data

Related structure data	8ezoC 8ezpC 8ezuC 8f00C 8f01C 8f03C 8f05C 8f06C 8f07C 8f0bC 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

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

1

Idetical with deposited unit
defined by author
Evidence: homology

Unit cell

Length a, b, c (Å)	77.706, 77.706, 37.121
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
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-355- 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 genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Production host: Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 75 / 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: 1.96 Å³/Da / Density % sol: 37.09 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 5 uL of 0.6 M Sodium Chloride in 100 mM Sodium Acetate buffer pH 4.5 and 25% ethylene glycol were mixed with 5 uL 100 mg/mL lysozyme in 100 mM Sodium Acetate.

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Data collection

Diffraction	Mean temperature: 293 K / Ambient temp details: Oxford Cryo / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.7462 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 19, 2020
Radiation	Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.7462 Å / Relative weight: 1
Reflection	Resolution: 1.9→38.883 Å / Num. obs: 8682 / % possible obs: 92.9 % / Redundancy: 5.6 % / B_iso Wilson estimate: 25.9 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.033 / R_pim(I) all: 0.022 / Net I/σ(I): 30.7
Reflection shell	Resolution: 1.9→1.94 Å / Redundancy: 5 % / R_merge(I) obs: 0.119 / Mean I/σ(I) obs: 9.9 / Num. unique obs: 2347 / CC_1/2: 0.984 / R_pim(I) all: 0.084 / % possible all: 78.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
XDS		data reduction
Aimless		data scaling
SHELXDE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.9→38.883 Å / Cor.coef. F_o:F_c: 0.975 / Cor.coef. F_o:F_c free: 0.965 / SU B: 5.22 / SU ML: 0.077 / Cross valid method: FREE R-VALUE / ESU R: 0.146 / ESU R Free: 0.124
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1664	457	5.264 %
R_work	0.1297	8225	-
all	0.132	-	-
obs	-	8682	92.293 %

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: 22.922 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.143 Å²	-0 Å²	-0 Å²
2-	-	0.143 Å²	-0 Å²
3-	-	-	-0.286 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→38.883 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1001	0	13	75	1089

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.011	1098
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	964
X-RAY DIFFRACTION	r_angle_refined_deg	1.565	1.64	1497
X-RAY DIFFRACTION	r_angle_other_deg	0.543	1.563	2253
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.676	5	147
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.441	5	16
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.047	10	187
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.262	10	58
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	156
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	1343
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	249
X-RAY DIFFRACTION	r_nbd_refined	0.239	0.2	245
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.204	0.2	835
X-RAY DIFFRACTION	r_nbtor_refined	0.181	0.2	528
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	535
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.403	0.2	52
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.36	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.108	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.074	0.2	5
X-RAY DIFFRACTION	r_nbd_other	0.18	0.2	46
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.185	0.2	8
X-RAY DIFFRACTION	r_mcbond_it	2.213	2.386	535
X-RAY DIFFRACTION	r_mcbond_other	2.213	2.384	535
X-RAY DIFFRACTION	r_mcangle_it	3.017	4.455	672
X-RAY DIFFRACTION	r_mcangle_other	3.022	4.463	673
X-RAY DIFFRACTION	r_scbond_it	3.96	3.222	563
X-RAY DIFFRACTION	r_scbond_other	3.958	3.23	564
X-RAY DIFFRACTION	r_scangle_it	5.886	5.645	815
X-RAY DIFFRACTION	r_scangle_other	5.883	5.652	816
X-RAY DIFFRACTION	r_lrange_it	7.882	19.33	1333
X-RAY DIFFRACTION	r_lrange_other	7.869	18.712	1325

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.9-1.95	0.24	34	0.147	513	X-RAY DIFFRACTION	78.2547
1.95-2.003	0.167	21	0.13	548	X-RAY DIFFRACTION	87.404
2.003-2.061	0.184	26	0.12	522	X-RAY DIFFRACTION	86.0283
2.061-2.125	0.156	42	0.122	526	X-RAY DIFFRACTION	91.1717
2.125-2.194	0.18	38	0.114	517	X-RAY DIFFRACTION	89.8058
2.194-2.271	0.134	23	0.12	485	X-RAY DIFFRACTION	89.4366
2.271-2.356	0.192	32	0.124	496	X-RAY DIFFRACTION	92.3077
2.356-2.452	0.267	26	0.129	488	X-RAY DIFFRACTION	93.1159
2.452-2.561	0.185	22	0.135	472	X-RAY DIFFRACTION	95
2.561-2.685	0.266	15	0.13	475	X-RAY DIFFRACTION	94.4123
2.685-2.83	0.165	28	0.138	436	X-RAY DIFFRACTION	96.8685
2.83-3	0.179	21	0.135	415	X-RAY DIFFRACTION	95.4048
3-3.206	0.237	14	0.133	399	X-RAY DIFFRACTION	96.2704
3.206-3.461	0.125	18	0.124	385	X-RAY DIFFRACTION	97.8155
3.461-3.788	0.116	26	0.107	347	X-RAY DIFFRACTION	98.4169
3.788-4.23	0.105	17	0.11	328	X-RAY DIFFRACTION	99.1379
4.23-4.875	0.133	20	0.113	292	X-RAY DIFFRACTION	99.0476
4.875-5.948	0.208	12	0.153	239	X-RAY DIFFRACTION	95.4373
5.948-8.315	0.164	16	0.173	205	X-RAY DIFFRACTION	100
8.315-38.883	0.202	6	0.198	137	X-RAY DIFFRACTION	99.3056

Refinement TLS params.

Method: refined / Origin x: 18.992 Å / Origin y: 40.289 Å / Origin z: -0.46 Å

	11	12	13	21	22	23	31	32	33
T	0.0026 Å²	0.0011 Å²	-0.0068 Å²	-	0.0016 Å²	-0.0031 Å²	-	-	0.0954 Å²
L	2.9272 °²	-1.6157 °²	-0.1633 °²	-	3.0883 °²	0.1887 °²	-	-	1.5855 °²
S	0.0444 Å °	0.0292 Å °	0.2031 Å °	-0.0597 Å °	-0.051 Å °	-0.0635 Å °	-0.0035 Å °	0.0043 Å °	0.0066 Å °

Refinement TLS group

Selection: ALL

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