PDB-7rz0: Hen egg-white lysozyme with ionic liquid ethanolammonium formate ...

ID or keywords:

Entry

Database: PDB / ID: 7rz0

Title

Hen egg-white lysozyme with ionic liquid ethanolammonium formate 6.7 mol%

Components

Lysozyme C

Keywords

HYDROLASE / lysozyme / ionic liquid / ethanolammonium formate

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: 1.38 Å

Authors

Han, Q. / Darmanin, C. / Drummond, C. / Greaves, T.

Funding support

1items

Citation

Journal: J Colloid Interface Sci / Year: 2023
Title: Probing ion-binding at a protein interface: Modulation of protein properties by ionic liquids.
Authors: Han, Q. / Su, Y. / Smith, K.M. / Binns, J. / Drummond, C.J. / Darmanin, C. / Greaves, T.L.

History

Deposition	Aug 27, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 1, 2023	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 2023	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_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Oct 25, 2023	Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.0	Nov 15, 2023	Group: Atomic model / Data collection Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2
Revision 2.1	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	7rz0.cif.gz	110.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7rz0.ent.gz		Display	PDB format
PDBx/mmJSON format	7rz0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7rz0_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	7rz0_full_validation.pdf.gz	1.7 MB	Display
Data in XML	7rz0_validation.xml.gz	8.5 KB	Display
Data in CIF	7rz0_validation.cif.gz	11.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rz/7rz0 ftp://data.pdbj.org/pub/pdb/validation_reports/rz/7rz0	HTTPS FTP

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Related structure data

Related structure data	7rxyC 7rydC 7rykC 7rz1C 7rz2C 7jmuS C: citing same article (ref.) S: Starting model for refinement
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) #9 - Sep 2000 Lysozyme similarity (4) #136 - Apr 2011 Nanobodies similarity (3) #222 - Jun 2018 Proteins and Nanoparticles similarity (3) #142 - Oct 2011 PDB Pioneers similarity (3)

Deposited unit

AAA: Lysozyme C

hetero molecules

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

1

Idetical with deposited unit
defined by software
Evidence: SAXS

Unit cell

Length a, b, c (Å)	76.790, 76.790, 38.310
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	AAA-339- HOH
2	1	AAA-353- 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-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH₂O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-ETA / ETHANOLAMINE Type: L-peptide COOH carboxy terminus / Mass: 61.083 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₇NO / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
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: 1.97 Å³/Da / Density % sol: 37.58 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: ethanolammonium formate 6.7 mol% (ca. 30wt%) in water

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: May 2, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 1.38→38.42 Å / Num. obs: 23925 / % possible obs: 100 % / Redundancy: 13.9 % / CC_1/2: 0.998 / Net I/σ(I): 16.2
Reflection shell	Resolution: 1.38→1.41 Å / Num. unique obs: 1195 / CC_1/2: 0.943 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
iMOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7JMU

7jmu

Resolution: 1.38→38.42 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.957 / SU B: 2.084 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.057
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1758	1223	5.112 %
R_work	0.1439	22701	-
all	0.146	-	-
obs	-	22701	99.992 %

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: 11.827 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.891 Å²	-0 Å²	-0 Å²
2-	-	0.891 Å²	-0 Å²
3-	-	-	-1.782 Å²

Refinement step

Cycle: LAST / Resolution: 1.38→38.42 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1000	0	19	114	1133

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.012	1103
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.018	1016
X-RAY DIFFRACTION	r_angle_refined_deg	2.055	1.632	1494
X-RAY DIFFRACTION	r_angle_other_deg	0.734	1.591	2290
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.182	5	142
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.758	20.441	68
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.907	15	177
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.261	15	13
X-RAY DIFFRACTION	r_chiral_restr	0.122	0.2	137
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	1339
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	310
X-RAY DIFFRACTION	r_nbd_refined	0.236	0.2	248
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.214	0.2	943
X-RAY DIFFRACTION	r_nbtor_refined	0.185	0.2	538
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	545
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.114	0.2	62
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.342	0.2	20
X-RAY DIFFRACTION	r_nbd_other	0.3	0.2	58
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.26	0.2	15
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.11	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	1.598	0.85	550
X-RAY DIFFRACTION	r_mcbond_other	1.459	0.85	549
X-RAY DIFFRACTION	r_mcangle_it	1.818	1.297	699
X-RAY DIFFRACTION	r_mcangle_other	1.881	1.299	699
X-RAY DIFFRACTION	r_scbond_it	2.96	1.215	552
X-RAY DIFFRACTION	r_scbond_other	2.942	1.206	541
X-RAY DIFFRACTION	r_scangle_it	3.471	1.686	795
X-RAY DIFFRACTION	r_scangle_other	3.454	1.683	790
X-RAY DIFFRACTION	r_lrange_it	3.376	11.205	1328
X-RAY DIFFRACTION	r_lrange_other	3.32	10.896	1309
X-RAY DIFFRACTION	r_rigid_bond_restr	5.373	3	2117

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 (%)
1.384-1.42	0.238	77	0.14	1667	X-RAY DIFFRACTION	100
1.42-1.459	0.192	71	0.129	1598	X-RAY DIFFRACTION	100
1.459-1.501	0.169	79	0.125	1564	X-RAY DIFFRACTION	100
1.501-1.547	0.157	88	0.122	1518	X-RAY DIFFRACTION	100
1.547-1.598	0.217	69	0.119	1509	X-RAY DIFFRACTION	100
1.598-1.654	0.235	68	0.107	1409	X-RAY DIFFRACTION	100
1.654-1.716	0.147	93	0.11	1368	X-RAY DIFFRACTION	100
1.716-1.786	0.163	88	0.105	1309	X-RAY DIFFRACTION	100
1.786-1.866	0.189	76	0.113	1283	X-RAY DIFFRACTION	100
1.866-1.957	0.186	73	0.139	1225	X-RAY DIFFRACTION	100
1.957-2.062	0.172	43	0.13	1175	X-RAY DIFFRACTION	100
2.062-2.187	0.136	58	0.131	1116	X-RAY DIFFRACTION	100
2.187-2.338	0.194	65	0.127	1037	X-RAY DIFFRACTION	100
2.338-2.525	0.192	53	0.142	992	X-RAY DIFFRACTION	100
2.525-2.765	0.233	41	0.162	924	X-RAY DIFFRACTION	100
2.765-3.091	0.169	49	0.167	814	X-RAY DIFFRACTION	100
3.091-3.567	0.158	44	0.169	738	X-RAY DIFFRACTION	100
3.567-4.364	0.128	37	0.151	632	X-RAY DIFFRACTION	99.8507
4.364-6.152	0.175	40	0.22	501	X-RAY DIFFRACTION	100

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