PDB-8f0b: Lysozyme Anomalous Dataset at 240 K and 7.1 keV

ID or keywords:

Entry

Database: PDB / ID: 8f0b

Title

Lysozyme Anomalous Dataset at 240 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 2, 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 30, 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	8f0b.cif.gz	45.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8f0b.ent.gz	29.2 KB	Display	PDB format
PDBx/mmJSON format	8f0b.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8f0b_validation.pdf.gz	429.6 KB	Display	wwPDB validaton report
Full document	8f0b_full_validation.pdf.gz	429.8 KB	Display
Data in XML	8f0b_validation.xml.gz	8.6 KB	Display
Data in CIF	8f0b_validation.cif.gz	11.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f0/8f0b ftp://data.pdbj.org/pub/pdb/validation_reports/f0/8f0b	HTTPS FTP

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Related structure data

Related structure data	8ezoC 8ezpC 8ezuC 8ezxC 8f00C 8f01C 8f03C 8f05C 8f06C 8f07C 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)	77.106, 77.106, 37.042
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-335- HOH
2	1	A-405- 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.: 2 / 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.: 105 / 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: 1.92 Å³/Da / Density % sol: 34.5 %
Crystal grow	Temperature: 293 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: 240 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→37.04 Å / Num. obs: 9246 / % possible obs: 100 % / Redundancy: 15.8 % / B_iso Wilson estimate: 27.6 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.053 / R_pim(I) all: 0.018 / Net I/σ(I): 35.4
Reflection shell	Resolution: 1.9→1.94 Å / Redundancy: 12.5 % / R_merge(I) obs: 0.169 / Mean I/σ(I) obs: 12.6 / Num. unique obs: 590 / CC_1/2: 0.993 / R_pim(I) all: 0.067 / % possible all: 100

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Processing

Software

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

Refinement

Method to determine structure:

SAD / Resolution: 1.9→34.507 Å / Cor.coef. F_o:F_c: 0.974 / Cor.coef. F_o:F_c free: 0.953 / SU B: 2.862 / SU ML: 0.086 / Cross valid method: FREE R-VALUE / ESU R: 0.139 / ESU R Free: 0.139
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1981	478	5.17 %
R_work	0.1368	8767	-
all	0.14	-	-
obs	-	9245	99.957 %

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: 21.646 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.469 Å²	0 Å²	0 Å²
2-	-	-0.469 Å²	0 Å²
3-	-	-	0.937 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→34.507 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1001	0	16	105	1122

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.011	1060
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	923
X-RAY DIFFRACTION	r_angle_refined_deg	1.475	1.636	1439
X-RAY DIFFRACTION	r_angle_other_deg	0.549	1.562	2153
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.63	5	137
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	10.913	5	13
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.775	10	176
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	17.223	10	54
X-RAY DIFFRACTION	r_chiral_restr	0.082	0.2	150
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	1277
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	235
X-RAY DIFFRACTION	r_nbd_refined	0.241	0.2	239
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.199	0.2	845
X-RAY DIFFRACTION	r_nbtor_refined	0.179	0.2	535
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	513
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.377	0.2	65
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.003	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.165	0.2	6
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.177	0.2	13
X-RAY DIFFRACTION	r_nbd_other	0.114	0.2	48
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.148	0.2	15
X-RAY DIFFRACTION	r_mcbond_it	3.451	4.23	525
X-RAY DIFFRACTION	r_mcbond_other	3.434	4.229	525
X-RAY DIFFRACTION	r_mcangle_it	3.866	7.866	657
X-RAY DIFFRACTION	r_mcangle_other	3.879	7.882	658
X-RAY DIFFRACTION	r_scbond_it	4.993	5.085	535
X-RAY DIFFRACTION	r_scbond_other	4.99	5.092	536
X-RAY DIFFRACTION	r_scangle_it	6.746	9.11	777
X-RAY DIFFRACTION	r_scangle_other	6.742	9.117	778
X-RAY DIFFRACTION	r_lrange_it	7.601	33.288	1321
X-RAY DIFFRACTION	r_lrange_other	7.497	31.094	1300

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
1.9-1.949	0.209	30	0.14	640	0.143	670	0.976	0.988	100	0.128
1.949-2.003	0.206	31	0.143	604	0.147	635	0.971	0.987	100	0.133
2.003-2.061	0.263	29	0.132	612	0.137	641	0.953	0.988	100	0.121
2.061-2.124	0.205	42	0.141	556	0.145	598	0.973	0.988	100	0.135
2.124-2.193	0.248	40	0.126	575	0.134	615	0.96	0.99	100	0.12
2.193-2.27	0.187	31	0.127	541	0.131	573	0.978	0.99	99.8255	0.12
2.27-2.355	0.254	30	0.12	529	0.126	560	0.963	0.991	99.8214	0.118
2.355-2.451	0.177	31	0.121	507	0.124	538	0.981	0.991	100	0.12
2.451-2.559	0.214	18	0.141	499	0.143	517	0.965	0.986	100	0.14
2.559-2.683	0.271	15	0.141	485	0.145	500	0.955	0.987	100	0.14
2.683-2.828	0.197	27	0.137	448	0.14	475	0.975	0.988	100	0.141
2.828-2.998	0.19	24	0.15	423	0.153	447	0.978	0.985	100	0.156
2.998-3.203	0.256	14	0.151	421	0.155	435	0.975	0.985	100	0.16
3.203-3.457	0.2	19	0.133	379	0.136	398	0.976	0.99	100	0.142
3.457-3.783	0.163	27	0.132	344	0.134	371	0.984	0.99	100	0.146
3.783-4.224	0.168	16	0.127	329	0.129	345	0.989	0.991	100	0.15
4.224-4.865	0.131	20	0.123	285	0.123	305	0.99	0.992	100	0.15
4.865-5.929	0.306	12	0.161	254	0.167	266	0.966	0.987	100	0.191
5.929-8.263	0.234	16	0.161	200	0.166	216	0.962	0.984	100	0.18
8.263-34.507	0.105	6	0.145	137	0.143	143	0.992	0.985	100	0.177

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