PDB-8f00: Lysozyme Anomalous Dataset at 293 K and 12 keV

ID or keywords:

Entry

Database: PDB / ID: 8f00

Title

Lysozyme Anomalous Dataset at 293 K and 12 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: 1.2 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 16, 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	8f00.cif.gz	95 KB	Display	PDBx/mmCIF format
PDB format	pdb8f00.ent.gz	55.5 KB	Display	PDB format
PDBx/mmJSON format	8f00.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8f00_validation.pdf.gz	436.4 KB	Display	wwPDB validaton report
Full document	8f00_full_validation.pdf.gz	438.2 KB	Display
Data in XML	8f00_validation.xml.gz	8.8 KB	Display
Data in CIF	8f00_validation.cif.gz	11.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f0/8f00 ftp://data.pdbj.org/pub/pdb/validation_reports/f0/8f00	HTTPS FTP

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Related structure data

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

14.8 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)	77.794, 77.794, 37.127
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-340- HOH
2	1	A-348- 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.: 10 / 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.: 89 / 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: 37.24 %
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: 1.0332 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: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 1.2→35.06 Å / Num. obs: 34193 / % possible obs: 95 % / Redundancy: 53.9 % / B_iso Wilson estimate: 22.153 Å² / CC_1/2: 1 / R_merge(I) obs: 0.092 / R_pim(I) all: 0.013 / Net I/σ(I): 27.9
Reflection shell	Resolution: 1.2→1.22 Å / Redundancy: 52.8 % / R_merge(I) obs: 5.75 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1567 / CC_1/2: 0.622 / R_pim(I) all: 0.79 / % possible all: 90.1

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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: 1.2→33.529 Å / Cor.coef. F_o:F_c: 0.986 / Cor.coef. F_o:F_c free: 0.981 / WR_factor R_free: 0.138 / WR_factor R_work: 0.115 / SU B: 1.409 / SU ML: 0.027 / Average fsc free: 0.9785 / Average fsc work: 0.9859 / Cross valid method: FREE R-VALUE / ESU R: 0.036 / ESU R Free: 0.035
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1462	1686	4.931 %
R_work	0.1209	32507	-
all	0.122	-	-
obs	-	34193	94.5 %

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: 23.629 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.299 Å²	-0 Å²	-0 Å²
2-	-	0.299 Å²	-0 Å²
3-	-	-	-0.599 Å²

Refinement step

Cycle: LAST / Resolution: 1.2→33.529 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1001	0	15	89	1105

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.011	1145
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.016	1016
X-RAY DIFFRACTION	r_angle_refined_deg	1.801	1.643	1568
X-RAY DIFFRACTION	r_angle_other_deg	0.661	1.567	2391
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.103	5	158
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.644	5	16
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.358	10	205
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.754	10	62
X-RAY DIFFRACTION	r_chiral_restr	0.098	0.2	163
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	1405
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	255
X-RAY DIFFRACTION	r_nbd_refined	0.263	0.2	246
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.212	0.2	844
X-RAY DIFFRACTION	r_nbtor_refined	0.182	0.2	545
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	545
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.452	0.2	54
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.157	0.2	3
X-RAY DIFFRACTION	r_metal_ion_refined	0.096	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.272	0.2	21
X-RAY DIFFRACTION	r_nbd_other	0.262	0.2	64
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.31	0.2	17
X-RAY DIFFRACTION	r_mcbond_it	4.731	3.957	549
X-RAY DIFFRACTION	r_mcbond_other	4.714	3.954	549
X-RAY DIFFRACTION	r_mcangle_it	4.958	7.454	692
X-RAY DIFFRACTION	r_mcangle_other	4.954	7.469	693
X-RAY DIFFRACTION	r_scbond_it	18.367	5.622	596
X-RAY DIFFRACTION	r_scbond_other	18.352	5.636	597
X-RAY DIFFRACTION	r_scangle_it	14.324	9.785	859
X-RAY DIFFRACTION	r_scangle_other	14.388	9.803	860
X-RAY DIFFRACTION	r_lrange_it	10.285	37.114	1393
X-RAY DIFFRACTION	r_lrange_other	10.3	35.02	1375
X-RAY DIFFRACTION	r_rigid_bond_restr	26.56	3	2161

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
1.2-1.231	0.289	121	0.266	2221	0.267	2620	0.947	0.963	89.3893	0.257
1.231-1.265	0.235	108	0.22	2219	0.22	2549	0.964	0.972	91.2907	0.207
1.265-1.302	0.249	113	0.203	2169	0.205	2502	0.953	0.973	91.207	0.188
1.302-1.342	0.218	115	0.193	2084	0.195	2425	0.971	0.976	90.6804	0.171
1.342-1.385	0.196	129	0.155	2071	0.158	2352	0.978	0.985	93.5374	0.136
1.385-1.434	0.175	100	0.142	2073	0.143	2291	0.981	0.987	94.8494	0.12
1.434-1.488	0.172	103	0.131	2007	0.133	2207	0.981	0.989	95.6049	0.113
1.488-1.549	0.164	84	0.12	1935	0.122	2112	0.984	0.991	95.5966	0.104
1.549-1.617	0.148	91	0.111	1868	0.113	2041	0.987	0.992	95.9824	0.095
1.617-1.696	0.123	87	0.107	1804	0.108	1958	0.991	0.993	96.5781	0.093
1.696-1.788	0.15	93	0.104	1613	0.107	1857	0.987	0.993	91.8686	0.091
1.788-1.896	0.133	76	0.095	1646	0.097	1775	0.99	0.995	97.0141	0.085
1.896-2.026	0.102	84	0.089	1539	0.089	1658	0.993	0.996	97.889	0.081
2.026-2.188	0.112	77	0.093	1452	0.094	1574	0.993	0.995	97.141	0.087
2.188-2.396	0.11	72	0.096	1362	0.097	1450	0.993	0.995	98.8966	0.092
2.396-2.677	0.109	62	0.105	1235	0.105	1319	0.993	0.993	98.3321	0.106
2.677-3.087	0.177	53	0.116	1067	0.119	1180	0.979	0.992	94.9153	0.123
3.087-3.773	0.126	48	0.109	911	0.109	1006	0.99	0.992	95.328	0.118
3.773-5.303	0.132	46	0.12	762	0.121	810	0.989	0.992	99.7531	0.144
5.303-33.529	0.248	24	0.191	469	0.194	494	0.954	0.976	99.7976	0.209

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