PDB-7ryk: Hen egg-white lysozyme with ionic liquid ethanolammonium nitrate ...

ID or keywords:

Entry

Database: PDB / ID: 7ryk

Title

Hen egg-white lysozyme with ionic liquid ethanolammonium nitrate 1 mol%

Components

Lysozyme C

Keywords

HYDROLASE / lysozyme / ionic liquid / ethanolammonium nitrate

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: 1.76 Å

Authors

Han, Q. / Darmanin, C. / Smith, K. / 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 25, 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 1.3	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7ryk.cif.gz	203.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7ryk.ent.gz		Display	PDB format
PDBx/mmJSON format	7ryk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7ryk_validation.pdf.gz	3.1 MB	Display	wwPDB validaton report
Full document	7ryk_full_validation.pdf.gz	3.1 MB	Display
Data in XML	7ryk_validation.xml.gz	13.5 KB	Display
Data in CIF	7ryk_validation.cif.gz	19 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ry/7ryk ftp://data.pdbj.org/pub/pdb/validation_reports/ry/7ryk	HTTPS FTP

-
Related structure data

Related structure data	7rxyC 7rydC 7rz0C 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

-
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

BBB: Lysozyme C

hetero molecules

29.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

AAA: Lysozyme C

hetero molecules

defined by author
Evidence: SAXS
14.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

BBB: Lysozyme C

hetero molecules

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

Unit cell

Length a, b, c (Å)	27.460, 62.350, 59.470
Angle α, β, γ (deg.)	90.000, 90.570, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV Mass: 14331.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical	ChemComp-NO3 / NITRATE ION Mass: 62.005 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: NO₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 1.78 Å³/Da / Density % sol: 30.75 %
Crystal grow	Temperature: 293.15 K / Method: microbatch / pH: 8 / Details: ethanolammonium nitrate 1mol% (ca. 7wt%) in water

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95372 Å / Relative weight: 1
Reflection	Resolution: 1.76→43.03 Å / Num. obs: 19931 / % possible obs: 99.9 % / Redundancy: 3.3 % / CC_1/2: 0.996 / Net I/σ(I): 8.5
Reflection shell	Resolution: 1.76→1.8 Å / Num. unique obs: 1414 / CC_1/2: 0.615 / % possible all: 100

-
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: 1.76→29.75 Å / Cor.coef. F_o:F_c: 0.974 / Cor.coef. F_o:F_c free: 0.933 / SU B: 8.506 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R Free: 0.139
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2243	960	4.8 %
R_work	0.1332	18942	-
all	0.138	-	-
obs	-	18942	99.75 %

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: 20.718 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.505 Å²	0 Å²	1.184 Å²
2-	-	-2.754 Å²	0 Å²
3-	-	-	1.225 Å²

Refinement step

Cycle: LAST / Resolution: 1.76→29.75 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2000	0	48	163	2211

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.013	2164
X-RAY DIFFRACTION	r_bond_other_d	0.005	0.018	1891
X-RAY DIFFRACTION	r_angle_refined_deg	1.666	1.634	2932
X-RAY DIFFRACTION	r_angle_other_deg	1.477	1.59	4371
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.45	5	274
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.065	20.308	130
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.419	15	351
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.747	15	25
X-RAY DIFFRACTION	r_chiral_restr	0.086	0.2	271
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	2534
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	521
X-RAY DIFFRACTION	r_nbd_refined	0.217	0.2	476
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.204	0.2	1776
X-RAY DIFFRACTION	r_nbtor_refined	0.171	0.2	1032
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	881
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.167	0.2	121
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.179	0.2	25
X-RAY DIFFRACTION	r_nbd_other	0.232	0.2	115
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.196	0.2	27
X-RAY DIFFRACTION	r_mcbond_it	3.297	1.977	1065
X-RAY DIFFRACTION	r_mcbond_other	3.109	1.973	1064
X-RAY DIFFRACTION	r_mcangle_it	4	2.97	1338
X-RAY DIFFRACTION	r_mcangle_other	4	2.973	1339
X-RAY DIFFRACTION	r_scbond_it	4.188	2.338	1099
X-RAY DIFFRACTION	r_scbond_other	4.071	2.311	1082
X-RAY DIFFRACTION	r_scangle_it	5.056	3.364	1589
X-RAY DIFFRACTION	r_scangle_other	4.977	3.335	1572
X-RAY DIFFRACTION	r_lrange_it	5.577	23.297	2569
X-RAY DIFFRACTION	r_lrange_other	5.497	23.101	2543
X-RAY DIFFRACTION	r_rigid_bond_restr	3.909	3	4055

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 (%)
1.761-1.807	0.261	64	0.188	1414	X-RAY DIFFRACTION	99.7301
1.807-1.856	0.317	64	0.19	1360	X-RAY DIFFRACTION	99.5108
1.856-1.91	0.265	71	0.181	1294	X-RAY DIFFRACTION	99.5624
1.91-1.969	0.307	95	0.165	1270	X-RAY DIFFRACTION	99.7078
1.969-2.033	0.258	47	0.143	1244	X-RAY DIFFRACTION	99.6911
2.033-2.104	0.264	38	0.145	1254	X-RAY DIFFRACTION	99.7683
2.104-2.184	0.242	38	0.129	1150	X-RAY DIFFRACTION	100
2.184-2.273	0.24	37	0.106	1163	X-RAY DIFFRACTION	99.6678
2.273-2.374	0.183	47	0.098	1069	X-RAY DIFFRACTION	99.8211
2.374-2.489	0.212	66	0.114	1028	X-RAY DIFFRACTION	99.8175
2.489-2.624	0.189	51	0.105	959	X-RAY DIFFRACTION	100
2.624-2.783	0.228	41	0.11	935	X-RAY DIFFRACTION	99.7955
2.783-2.974	0.222	45	0.124	881	X-RAY DIFFRACTION	99.8921
2.974-3.212	0.21	43	0.138	794	X-RAY DIFFRACTION	99.8807
3.212-3.517	0.21	60	0.129	739	X-RAY DIFFRACTION	99.875
3.517-3.931	0.149	40	0.11	688	X-RAY DIFFRACTION	99.8628
3.931-4.536	0.265	38	0.109	592	X-RAY DIFFRACTION	100
4.536-5.547	0.195	36	0.155	487	X-RAY DIFFRACTION	99.241
5.547-7.811	0.203	16	0.167	398	X-RAY DIFFRACTION	99.759

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi