PDB-8q5u: Endoglycosidase S2 in complex with IgG1 Fc

ID or keywords:

Entry

Database: PDB / ID: 8q5u

Title

Endoglycosidase S2 in complex with IgG1 Fc

Components

Endo-beta-N-acetylglucosaminidase
Uncharacterized protein DKFZp686C11235

Keywords

IMMUNE SYSTEM / Antibody / IgG / Fc / endoglycosidase S2 / EndoS2

Function / homology

Function and homology information

mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / immunoglobulin complex / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / adaptive immune response / extracellular region / metal ion binding / plasma membrane
Similarity search - Function

Biological species

Homo sapiens (human)

Streptococcus pyogenes (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3 Å

Authors

Sudol, A.S.L. / Tews, I. / Crispin, M.

Funding support

United Kingdom, 1items

Citation

Journal: J.Biol.Chem. / Year: 2024
Title: The IgG-specific endoglycosidases EndoS and EndoS2 are distinguished by conformation and antibody recognition.
Authors: Sudol, A.S.L. / Crispin, M. / Tews, I.

History

Deposition	Aug 9, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 17, 2024	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2024	Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2	Oct 9, 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	8q5u.cif.gz	2.5 MB	Display	PDBx/mmCIF format
PDB format	pdb8q5u.ent.gz	1.6 MB	Display	PDB format
PDBx/mmJSON format	8q5u.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/q5/8q5u ftp://data.pdbj.org/pub/pdb/validation_reports/q5/8q5u	HTTPS FTP

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Related structure data

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 (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: Uncharacterized protein DKFZp686C11235

D: Endo-beta-N-acetylglucosaminidase

C: Uncharacterized protein DKFZp686C11235

E: Endo-beta-N-acetylglucosaminidase

F: Endo-beta-N-acetylglucosaminidase

B: Uncharacterized protein DKFZp686C11235

hetero molecules

358 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: One enzyme interacts with one chain of an IgG1 Fc homodimer (therefore two enzyme copies interact with one Fc homodimer)

Unit cell

Length a, b, c (Å)	228.775, 228.775, 161.629
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	2	F
3	3	C
4	4	B
5	5	D
6	6	E

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	GLY	GLY	LEU	LEU	A	A	237 - 443	17 - 223
2	2	2	GLY	GLY	SER	SER	B	F	237 - 444	17 - 224
3	3	3	GLY	GLY	LEU	LEU	C	C	237 - 443	17 - 223
4	4	4	HIS	HIS	GLN	GLN	D	B	371 - 831	335 - 795
5	5	5	ASN	ASN	GLN	GLN	E	D	265 - 831	229 - 795
6	6	6	THR	THR	ARG	ARG	F	E	46 - 832	10 - 796

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

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Protein , 2 types, 6 molecules ACBDEF

#1: Protein	Uncharacterized protein DKFZp686C11235 Mass: 25544.967 Da / Num. of mol.: 3 / Mutation: L234C E382A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DKFZp686C11235 / Cell line (production host): Freestyle HEK293-F cells / Production host: Homo sapiens (human) / References: UniProt: Q6MZV7
#2: Protein	Endo-beta-N-acetylglucosaminidase Mass: 92581.242 Da / Num. of mol.: 3 / Mutation: D184A E186L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: endoS / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8H2N1T2

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Sugars , 2 types, 2 molecules

#3: Polysaccharide

2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...

Type: oligosaccharide / Mass: 1463.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/4,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-1-3-1-4/a4-b1_a6-h1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}[(6+1)][a-L-Fucp]{}}	LINUCS	PDB-CARE

#4: Polysaccharide

2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose- ...

Type: oligosaccharide / Mass: 1260.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DGlcpNAcb1-2DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/4,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-1-4/a4-b1_a6-g1_b4-c1_c3-d1_c6-e1_e2-f1	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}[(6+1)][a-L-Fucp]{}}	LINUCS	PDB-CARE

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Non-polymers , 4 types, 293 molecules

#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#7: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.98 Å³/Da / Density % sol: 58.78 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: Morpheus (Molecular Dimensions) conditon G12: 0.1 M carboxylic acids(0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Potassium sodium tartrate ...Details: Morpheus (Molecular Dimensions) conditon G12: 0.1 M carboxylic acids(0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Potassium sodium tartrate tetrahydrate; 0.2M Sodium oxamate); 0.1 M buffer system 3(Tris (base); BICINE); pH 8.5; 37.5 v/v Precipitant Mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350)

Crystal

Density Matthews: 2.98 Å³/Da / Density % sol: 58.78 %

Crystal grow

Temperature: 298 K / Method: vapor diffusion, sitting drop
Details: Morpheus (Molecular Dimensions) conditon G12: 0.1 M carboxylic acids(0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Potassium sodium tartrate ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 24, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 3→49.91 Å / Num. obs: 85926 / % possible obs: 100 % / Redundancy: 27.5 % / B_iso Wilson estimate: 77 Å² / CC_1/2: 1 / R_merge(I) obs: 0.187 / R_pim(I) all: 0.036 / R_rim(I) all: 0.191 / Net I/σ(I): 12.6
Reflection shell	Resolution: 3→3.05 Å / R_merge(I) obs: 2.614 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 4250 / CC_1/2: 0.64 / R_pim(I) all: 0.527 / R_rim(I) all: 2.668 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
DIALS		data reduction
DIALS		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3→49.91 Å / Cor.coef. F_o:F_c: 0.927 / Cor.coef. F_o:F_c free: 0.918 / SU B: 46.453 / SU ML: 0.384 / Cross valid method: FREE R-VALUE / ESU R Free: 0.391
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2516	4376	5.097 %
R_work	0.2161	81473	-
all	0.218	-	-
obs	-	85849	99.956 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 100.098 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.691 Å²	-0 Å²	-0 Å²
2-	-	-0.691 Å²	-0 Å²
3-	-	-	1.382 Å²

Refinement step

Cycle: LAST / Resolution: 3→49.91 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20629	0	258	281	21168

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.003	0.012	21304
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	19739
X-RAY DIFFRACTION	r_angle_refined_deg	0.957	1.666	28858
X-RAY DIFFRACTION	r_angle_other_deg	0.526	1.596	45579
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.462	5	2607
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.77	5	87
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.787	10	3634
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.837	10	994
X-RAY DIFFRACTION	r_chiral_restr	0.059	0.2	3249
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	24908
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4723
X-RAY DIFFRACTION	r_nbd_refined	0.182	0.2	3814
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.195	0.2	18793
X-RAY DIFFRACTION	r_nbtor_refined	0.172	0.2	10339
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	11390
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.203	0.2	496
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.024	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.11	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.167	0.2	19
X-RAY DIFFRACTION	r_nbd_other	0.16	0.2	102
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.169	0.2	16
X-RAY DIFFRACTION	r_mcbond_it	1.41	5.84	10482
X-RAY DIFFRACTION	r_mcbond_other	1.41	5.84	10482
X-RAY DIFFRACTION	r_mcangle_it	2.428	10.496	13071
X-RAY DIFFRACTION	r_mcangle_other	2.428	10.496	13072
X-RAY DIFFRACTION	r_scbond_it	1.496	6.053	10822
X-RAY DIFFRACTION	r_scbond_other	1.496	6.054	10823
X-RAY DIFFRACTION	r_scangle_it	2.648	11.07	15787
X-RAY DIFFRACTION	r_scangle_other	2.648	11.07	15788
X-RAY DIFFRACTION	r_lrange_it	6.25	70.424	87367
X-RAY DIFFRACTION	r_lrange_other	6.244	70.418	87302
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.108	0.05	5883
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.104	0.05	5981
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.095	0.05	13448
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.09	0.05	24971
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.104	0.05	5847
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.1	0.05	13438

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.10825	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.10825	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.1035	0.05009
2	4	A	X-RAY DIFFRACTION	Local ncs	0.1035	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.09532	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.09532	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.08952	0.05011
4	8	A	X-RAY DIFFRACTION	Local ncs	0.08952	0.05011
5	9	A	X-RAY DIFFRACTION	Local ncs	0.104	0.05009
5	10	A	X-RAY DIFFRACTION	Local ncs	0.104	0.05009
6	11	A	X-RAY DIFFRACTION	Local ncs	0.09998	0.0501
6	12	A	X-RAY DIFFRACTION	Local ncs	0.09998	0.0501

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 (%)
3-3.078	0.352	297	0.351	5938	X-RAY DIFFRACTION	99.984
3.078-3.162	0.326	306	0.333	5777	X-RAY DIFFRACTION	100
3.162-3.253	0.284	273	0.291	5676	X-RAY DIFFRACTION	100
3.253-3.353	0.294	283	0.264	5468	X-RAY DIFFRACTION	99.9826
3.353-3.462	0.268	296	0.252	5297	X-RAY DIFFRACTION	100
3.462-3.583	0.27	309	0.234	5113	X-RAY DIFFRACTION	100
3.583-3.717	0.261	283	0.213	4923	X-RAY DIFFRACTION	100
3.717-3.868	0.217	265	0.202	4780	X-RAY DIFFRACTION	100
3.868-4.039	0.228	249	0.185	4609	X-RAY DIFFRACTION	100
4.039-4.235	0.222	251	0.172	4396	X-RAY DIFFRACTION	100
4.235-4.462	0.22	232	0.167	4196	X-RAY DIFFRACTION	100
4.462-4.731	0.198	206	0.161	3986	X-RAY DIFFRACTION	100
4.731-5.054	0.223	197	0.171	3778	X-RAY DIFFRACTION	100
5.054-5.454	0.232	178	0.174	3512	X-RAY DIFFRACTION	100
5.454-5.968	0.241	161	0.198	3249	X-RAY DIFFRACTION	100
5.968-6.66	0.28	175	0.222	2946	X-RAY DIFFRACTION	100
6.66-7.668	0.277	144	0.22	2645	X-RAY DIFFRACTION	100
7.668-9.337	0.256	122	0.226	2245	X-RAY DIFFRACTION	99.7472
9.337-12.979	0.269	88	0.227	1810	X-RAY DIFFRACTION	100
12.979-49.91	0.278	61	0.313	1129	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.5748	-0.1959	-0.0161	0.7864	0.2305	0.5885	-0.0534	0.2109	0.2282	-0.0877	-0.0689	-0.0009	-0.108	-0.088	0.1223	0.1077	-0.086	-0.0062	0.1735	0.0494	0.4408	34.888	-8.6108	-47.8801
2	0.6421	-0.3084	-0.2628	0.8566	-0.6244	1.3603	-0.1559	-0.3783	-0.1357	0.2491	-0.0803	-0.268	0.2051	0.2994	0.2362	0.7305	0.024	-0.0624	0.5432	-0.0529	0.9144	99.7087	-13.7726	23.8975
3	0.2817	-0.0325	0.4299	0.7851	-0.065	0.7532	0.0864	-0.1555	0.1559	0.0559	-0.2051	0.0219	0.1297	-0.1512	0.1187	0.5931	0.0119	0.0548	0.3163	-0.0289	0.5498	89.7462	-51.0462	7.7634
4	2.4705	0.7942	0.6549	2.6107	0.8235	2.0521	0.0235	0.17	-0.0199	0.0149	-0.0972	0.3688	0.3289	-0.1941	0.0737	0.1887	0.0034	-0.0494	0.0574	-0.0512	0.3337	48.5547	12.2687	-15.3997
5	1.6907	-1.1257	0.5149	4.6445	0.4456	1.0428	0.1311	-0.1018	-0.2756	0.2218	-0.0528	-0.04	0.4553	0.0433	-0.0782	0.2726	-0.0085	-0.0387	0.129	0.0117	0.3085	74.4081	8.4504	-7.0246
6	1.4258	-0.0062	0.0314	4.5198	0.178	1.1685	-0.0654	0.3085	0.1162	0.024	-0.0987	-0.1221	-0.211	-0.1958	0.1641	0.528	-0.1059	-0.0951	0.7149	0.0848	0.4985	94.6546	-75.0776	38.6795

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	4	ALL	A	237 - 340
2	X-RAY DIFFRACTION	4	ALL	A	341 - 444

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Components

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Protein , 2 types, 6 molecules ACBDEF

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Sugars , 2 types, 2 molecules

-
Non-polymers , 4 types, 293 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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-Protein , 2 types, 6 molecules ACBDEF

-Sugars , 2 types, 2 molecules

-Non-polymers , 4 types, 293 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

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+About Yorodumi

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

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Protein , 2 types, 6 molecules ACBDEF

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Sugars , 2 types, 2 molecules

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Non-polymers , 4 types, 293 molecules

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