PDB-30ig: EVAL processed HEWL, N-acetylglucosamine

ID or keywords:

Entry

Database: PDB / ID: 30ig

Title

EVAL processed HEWL, N-acetylglucosamine

Components

Lysozyme C

Keywords

HYDROLASE / hen egg white lysozyme (HEWL) / platinum / N-acetylglucosamine

Function / homology

Function and homology information

Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to bacterium ...
Similarity search - Function

Biological species

Gallus gallus (chicken)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Tanley, S.W. / Kroon-Batenburg, L. / Joosten, R.P. / Helliwell, J.R.

Funding support

United Kingdom, 1items

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structural studies of the effect that dimethyl sulfoxide (DMSO) has on cisplatin and carboplatin binding to histidine in a protein.
Authors: Tanley, S.W. / Kroon-Batenburg, L.M. / Helliwell, J.R.

History

Deposition	Apr 28, 2026	Deposition site: PDBE / Processing site: PDBE
Supersession	Jun 17, 2026	ID: 4DDA
Revision 1.0	Jun 17, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	30ig.cif.gz	80.6 KB	Display	PDBx/mmCIF format
PDB format	pdb30ig.ent.gz	49.3 KB	Display	PDB format
PDBx/mmJSON format	30ig.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/0i/30ig ftp://data.pdbj.org/pub/pdb/validation_reports/0i/30ig	HTTPS FTP

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Related structure data

Related structure data	4dd0C 4dd1C 4dd2C 4dd3C 4dd7C 4dd9C 4ddbC 4ddcC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.5281/zenodo.18258544 / Data set type: diffraction image data

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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) #99 - Mar 2008 Cadherin similarity (1) #142 - Oct 2011 PDB Pioneers similarity (3) #76 - Apr 2006 Hemagglutinin similarity (1) #83 - Nov 2006 Fibrin similarity (1)

Deposited unit

A: Lysozyme C

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	78.392, 78.392, 36.578
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	96
Space group name H-M	P4₃2₁2

#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) / Tissue: egg white / 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: Sugar

ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₅NO₆ / Feature type: SUBJECT OF INVESTIGATION

Identifier	Type	Program
DGlcpNAca	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-a-D-glucopyranosamine	COMMON NAME	GMML 1.0
a-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 84 / 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: 1.96 Å³/Da / Density % sol: 37.25 %
Crystal grow	Temperature: 295 K / Method: batch mode / pH: 4.7 Details: HEWL CO-CRYSTALLIZED WITH 150 MM EXCESS N-ACETYLGLUCOSAMINE IN 1 ML 0.05 M SODIUM ACETATE AND 1 ML 10% SODIUM CHLORIDE, PH 4.7, BATCH, TEMPERATURE 295K Temp details: Room temperature

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54184 Å
Detector	Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 1, 2011 / Details: OSMIC CONFOCAL MAX-FLUX, BLUE
Radiation	Monochromator: confocal mirror optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54184 Å / Relative weight: 1
Reflection	Resolution: 2→19.606 Å / Num. obs: 7468 / % possible obs: 91.5 % / Redundancy: 12.46 % / B_iso Wilson estimate: 23.8 Å² / CC_1/2: 0.996 / CC star: 0.999 / R_pim(I) all: 0.073 / R_rim(I) all: 0.253 / R_sym value: 0.243 / Χ²: 1 / Net I/av σ(I): 11.17 / Net I/σ(I): 8.15
Reflection shell	Resolution: 2→2.071 Å / Redundancy: 12.76 % / Mean I/σ(I) obs: 1.14 / Num. unique obs: 796 / CC_1/2: 0.508 / CC star: 0.821 / R_pim(I) all: 0.569 / R_rim(I) all: 2.04 / R_sym value: 1.96 / Χ²: 0.66 / % possible all: 91.5

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0431 (refmacat 0.4.123)	refinement
PDB-REDO	8.22	refinement
EVAL15		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→19.606 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.928 / SU B: 13.461 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.306 / ESU R Free: 0.226
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2595	753	10.125 %	RANDOM
R_work	0.2038	6684	-	-
all	0.209	-	-	-
obs	-	7437	91.431 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 21.853 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.186 Å²	-0 Å²	-0 Å²
2-	-	1.186 Å²	-0 Å²
3-	-	-	-2.371 Å²

Refinement step

Cycle: LAST / Resolution: 2→19.606 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1001	0	24	84	1109

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.016	1040
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	946
X-RAY DIFFRACTION	r_angle_refined_deg	0.964	1.788	1428
X-RAY DIFFRACTION	r_angle_other_deg	0.349	1.576	2158
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.594	5.396	139
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.648	10	166
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.998	10	50
X-RAY DIFFRACTION	r_chiral_restr	0.038	0.2	149
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	1279
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	281
X-RAY DIFFRACTION	r_nbd_refined	0.197	0.2	264
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.187	0.2	904
X-RAY DIFFRACTION	r_nbtor_refined	0.167	0.2	530
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	540
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.13	0.2	65
X-RAY DIFFRACTION	r_metal_ion_refined	0.017	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.101	0.2	9
X-RAY DIFFRACTION	r_nbd_other	0.135	0.2	53
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.099	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	1.02	1.957	515
X-RAY DIFFRACTION	r_mcbond_other	1.02	1.957	515
X-RAY DIFFRACTION	r_mcangle_it	1.757	3.565	652
X-RAY DIFFRACTION	r_mcangle_other	1.754	3.563	652
X-RAY DIFFRACTION	r_scbond_it	1.644	2.205	525
X-RAY DIFFRACTION	r_scbond_other	1.643	2.205	526
X-RAY DIFFRACTION	r_scangle_it	2.837	3.98	779
X-RAY DIFFRACTION	r_scangle_other	2.835	3.979	780
X-RAY DIFFRACTION	r_lrange_it	5.28	21.152	1307
X-RAY DIFFRACTION	r_lrange_other	5.265	20.547	1293

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
2-2.052	0.293	45	0.319	544	0.317	589	0.925	0.921	100	0.297
2.052-2.107	0.32	61	0.284	507	0.288	568	0.921	0.941	100	0.257
2.107-2.168	0.355	53	0.277	490	0.285	543	0.897	0.946	100	0.247
2.168-2.234	0.352	57	0.276	472	0.284	529	0.925	0.947	100	0.24
2.234-2.306	0.279	53	0.253	478	0.256	531	0.947	0.955	100	0.212
2.306-2.386	0.369	46	0.262	449	0.271	495	0.907	0.953	100	0.214
2.386-2.474	0.318	66	0.253	426	0.263	492	0.94	0.954	100	0.206
2.474-2.573	0.295	43	0.22	417	0.227	460	0.94	0.967	100	0.173
2.573-2.686	0.372	54	0.226	405	0.243	459	0.928	0.966	100	0.191
2.686-2.814	0.402	23	0.222	207	0.239	447	0.935	0.966	51.4541	0.175
2.814-2.963	0.235	23	0.212	224	0.215	403	0.966	0.972	61.2903	0.177
2.963-3.138	0.249	34	0.201	368	0.205	402	0.961	0.972	100	0.169
3.138-3.349	0.34	8	0.176	66	0.194	385	0.941	0.98	19.2208	0.15
3.349-3.609	0.234	44	0.181	302	0.188	346	0.958	0.979	100	0.173
3.609-3.94	0.219	32	0.155	294	0.16	326	0.963	0.984	100	0.15
3.94-4.383	0.129	29	0.14	271	0.138	300	0.986	0.987	100	0.147
4.383-5.019	0.2	29	0.167	243	0.17	272	0.974	0.984	100	0.171
5.019-6.049	0.213	24	0.149	216	0.154	240	0.975	0.987	100	0.148
6.049-8.174	0.296	23	0.164	169	0.177	192	0.955	0.981	100	0.171
8.174-19.606	0.174	6	0.217	136	0.214	142	0.981	0.973	100	0.244

Refinement TLS params.

Method: refined / Origin x: -0.921 Å / Origin y: 20.299 Å / Origin z: 18.436 Å

	11	12	13	21	22	23	31	32	33
T	0.0044 Å²	-0.0011 Å²	-0.0235 Å²	-	0.0123 Å²	-0.0068 Å²	-	-	0.2554 Å²
L	2.9919 °²	-1.5091 °²	-0.2878 °²	-	3.2269 °²	-0.3975 °²	-	-	1.7518 °²
S	0.0473 Å °	-0.0595 Å °	-0.1262 Å °	-0.0424 Å °	0.009 Å °	0.4131 Å °	-0.0025 Å °	-0.1174 Å °	-0.0563 Å °

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	1 - 129
2	X-RAY DIFFRACTION	1	ALL	A	210

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