PDB-4aml: CRYSTAL STRUCTURE OF WHEAT GERM AGGLUTININ ISOLECTIN 1 IN COMPLEX...

ID or keywords:

Entry

Database: PDB / ID: 4aml

Title

CRYSTAL STRUCTURE OF WHEAT GERM AGGLUTININ ISOLECTIN 1 IN COMPLEX WITH GLYCOSYLURETHAN

Components

AGGLUTININ ISOLECTIN 1

Keywords

SUGAR BINDING PROTEIN / SYNTHETIC CARBOHYDRATE LIGAND / PROTEIN CARBOHYDRATE INTERACTION / LECTIN / CHITIN-BINDING / CARBOHYDRATE BINDING PROTEIN

Function / homology

Function and homology information

chitin binding / carbohydrate binding
Similarity search - Function

Biological species

TRITICUM AESTIVUM (bread wheat)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Schwefel, D. / Maierhofer, C. / Beck, J.G. / Seeberger, S. / Diederichs, K. / Moeller, H.M. / Welte, W. / Wittmann, V.

Citation

Journal: J.Am.Chem.Soc. / Year: 2010
Title: Structural Basis of Multivalent Binding to Wheat Germ Agglutinin.
Authors: Schwefel, D. / Maierhofer, C. / Beck, J.G. / Seeberger, S. / Diederichs, K. / Moller, H.M. / Welte, W. / Wittmann, V.

History

Deposition	Mar 12, 2012	Deposition site: PDBE / Processing site: PDBE
Supersession	Apr 4, 2012	ID: 2UWG
Revision 1.0	Apr 4, 2012	Provider: repository / Type: Initial release
Revision 2.0	Mar 11, 2020	Group: Derived calculations / Other / Polymer sequence / Category: entity_poly / pdbx_database_status / struct_conn Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1	Jun 3, 2020	Group: Derived calculations Category: pdbx_struct_sheet_hbond / struct_conf ...pdbx_struct_sheet_hbond / struct_conf / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site Item: _pdbx_struct_sheet_hbond.sheet_id / _struct_conf.pdbx_PDB_helix_id ..._pdbx_struct_sheet_hbond.sheet_id / _struct_conf.pdbx_PDB_helix_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id / _struct_sheet.id / _struct_sheet_order.sheet_id / _struct_sheet_range.sheet_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 3.0	Jul 29, 2020	Group: Atomic model / Derived calculations / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4aml.cif.gz	139.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4aml.ent.gz	111.5 KB	Display	PDB format
PDBx/mmJSON format	4aml.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4aml_validation.pdf.gz	2 MB	Display	wwPDB validaton report
Full document	4aml_full_validation.pdf.gz	2.1 MB	Display
Data in XML	4aml_validation.xml.gz	19.2 KB	Display
Data in CIF	4aml_validation.cif.gz	26.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/am/4aml ftp://data.pdbj.org/pub/pdb/validation_reports/am/4aml	HTTPS FTP

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Related structure data

Related structure data	2uvoC 2x3tC 2x52C 7wgaS 1wgc 2cwg C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2x3t-1 2uvo-2 9wga-3 1k7t-d 1k7u-d 2x3t-2 1k7v-d 1k7v-2 9wga-1 2wgc-1 Search similar-shape structures by Omokage search (details) 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

Deposited unit

A: AGGLUTININ ISOLECTIN 1

B: AGGLUTININ ISOLECTIN 1

hetero molecules

35.7 kDa, 2 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)	63.250, 63.250, 153.550
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

#1: Protein	AGGLUTININ ISOLECTIN 1 / ISOLECTIN A / WGA1 Mass: 17124.080 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TRITICUM AESTIVUM (bread wheat) / References: UniProt: P10968
#2: Sugar	ChemComp-GYU / 2-acetamido-2-deoxy-1-O-(propylcarbamoyl)-alpha-D-glucopyranose / 2-(ACETYLAMINO)-2-DEOXY-1-O-(PROPYLCARBAMOYL)-ALPHA-D-GLUCOPYRANOSE / N-acetyl-1-O-(propylcarbamoyl)-alpha-D-glucosamine / 2-acetamido-2-deoxy-1-O-(propylcarbamoyl)-alpha-D-glucose / 2-acetamido-2-deoxy-1-O-(propylcarbamoyl)-D-glucose / 2-acetamido-2-deoxy-1-O-(propylcarbamoyl)-glucose Type: D-saccharide / Mass: 306.312 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₂H₂₂N₂O₇
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	THE PRECURSOR IS PROCESSED TO THE MATURE PROTEIN COMPRISING AMINO ACID RESIDUES 27 TO 197. RESIDUE ...THE PRECURSOR IS PROCESSED TO THE MATURE PROTEIN COMPRISING AMINO ACID RESIDUES 27 TO 197. RESIDUE 27 IS MODIFIED TO PYROGLUTAMIC ACID.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.59 Å³/Da / Density % sol: 52.44 % / Description: NONE
Crystal grow	Details: 0.04 M POTASSIUM PHOSPHATE 14 % PEG 8000 20 % GLYCEROL

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 27, 2006
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.6→10 Å / Num. obs: 46032 / % possible obs: 96.1 % / Observed criterion σ(I): 2 / Redundancy: 9.53 % / R_merge(I) obs: 0.06 / Net I/σ(I): 17.38
Reflection shell	Resolution: 1.6→1.65 Å / Redundancy: 8.3 % / R_merge(I) obs: 0.47 / Mean I/σ(I) obs: 3.52 / % possible all: 89.8

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Processing

Software

Name	Version	Classification
REFMAC	5.6.0117	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 7WGA

7wga

Resolution: 1.6→54.78 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.948 / SU B: 3.836 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23194	2317	5.1 %	RANDOM
R_work	0.19645	-	-	-
obs	0.19819	43469	95.58 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 33.462 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.5 Å²	0.75 Å²	0 Å²
2-	-	1.5 Å²	0 Å²
3-	-	-	-2.24 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→54.78 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2329	0	96	245	2670

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.021	0.019	2518
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.119	1.982	3385
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.191	5	339
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.052	25.417	96
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.784	15	337
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	7.433	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.139	0.2	311
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.021	1950
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.6→1.642 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.283	134	-
R_work	0.264	2376	-
obs	-	-	75.15 %

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	2.0918	4.6384	1.5336	10.3034	3.4404	2.6713	-0.0365	0.0161	0.0248	0.0157	0.0101	0.0236	0.1851	-0.1108	0.0264	0.2356	-0.0798	-0.0306	0.0833	-0.0318	0.1524	-22.5706	17.2753	5.2975
2	1.1895	0.5027	0.04	0.7613	-0.0016	1.1892	-0.1391	-0.0071	-0.0243	-0.1023	0.0741	0.0069	0.0219	0.0541	0.065	0.1981	-0.0754	0.0068	0.0463	0.0033	0.1379	-16.9517	19.7657	3.6199
3	2.038	0.773	-2.1985	3.0177	-0.7326	3.3091	-0.0501	0.1389	0.1187	-0.1886	0.1512	0.1856	-0.0282	-0.1036	-0.1011	0.2187	-0.1125	0.0014	0.0646	-0.0001	0.1472	-17.3082	25.6896	-1.5031
4	0.4889	0.8026	-0.5809	1.8582	-0.3653	1.3932	0.0449	-0.0234	0.0663	0.1665	-0.0109	0.1088	-0.0346	0.1068	-0.034	0.1707	-0.0881	0.0164	0.0571	-0.0092	0.1408	-12.3183	34.1255	10.5917
5	1.658	-0.0827	0.5256	0.917	-0.2828	1.3891	0.0567	-0.0583	0.0526	0.1697	-0.0711	-0.0004	-0.0274	0.3448	0.0144	0.2305	-0.1143	-0.0122	0.1607	-0.0026	0.1292	-2.8559	33.9273	14.4249
6	2.0079	0.9448	-1.502	5.3179	-0.5973	5.3025	0.2538	-0.1099	0.3515	0.4285	-0.1717	0.1928	-0.6272	0.2349	-0.082	0.3129	-0.0811	-0.0025	0.1254	-0.0459	0.0881	-6.3803	29.5382	30.9215
7	6.5793	0.0975	2.7671	3.1825	1.4794	5.16	-0.1141	-0.1893	0.1407	0.4332	0.0499	0.0344	-0.1669	0.4824	0.0642	0.2459	-0.0643	-0.0086	0.174	0.0041	0.0432	-3.5747	22.5898	28.4979
8	2.1712	0.7686	-0.3105	0.8499	0.0844	3.2404	0.0482	-0.4019	-0.0697	0.3558	-0.1775	-0.1442	0.1656	0.4832	0.1293	0.2436	-0.0097	-0.0511	0.1707	0.0373	0.0457	-3.256	18.5695	29.2
9	8.4983	-0.9638	-5.6062	0.1501	1.3003	14.8533	-0.0839	-0.3807	-0.2556	0.0316	-0.0004	0.0207	0.1696	-0.5998	0.0843	0.3015	-0.055	0.0222	0.2941	0.0787	0.0484	-17.2938	11.5363	40.4299
10	6.9927	0.0525	1.3117	0.672	1.9311	6.181	-0.1087	-0.2876	-0.1105	0.1615	-0.1345	0.075	0.4085	-0.6923	0.2432	0.2106	-0.0493	0.079	0.2056	-0.0362	0.0445	-21.5969	13.6788	30.4064
11	2.0195	0.4692	1.689	2.4548	0.8441	3.3912	-0.054	0.0365	0.0025	-0.057	0.0141	0.2127	0.3287	0.2108	0.0399	0.234	-0.0175	0.0279	0.0446	0.015	0.1192	-14.4905	12.2649	11.0058
12	3.8575	0.8114	2.5088	4.6845	4.1549	6.313	0.1436	-0.3481	-0.3165	0.1545	-0.1481	0.1418	0.6391	-0.1455	0.0046	0.2907	-0.011	0.042	0.0604	0.0516	0.1292	-15.7784	6.9591	16.6366
13	2.2943	0.8949	-0.5832	1.6066	0.4581	5.4076	-0.0559	-0.445	-0.2402	0.1409	-0.1386	-0.0499	0.6307	0.0038	0.1945	0.32	0.0042	0.0387	0.1408	0.055	0.1433	-12.2877	7.4556	22.8404
14	2.3217	0.9486	1.3243	1.1147	-0.2069	1.7024	-0.1048	0.2626	-0.0791	-0.1671	-0.0098	-0.0759	0.1864	0.4757	0.1147	0.2024	0.1161	0.0747	0.3013	0.0959	0.1082	1.0127	14.7114	15.7715
15	1.451	0.8457	-1.3139	5.5791	-4.2117	3.5491	-0.0302	-0.1952	-0.086	0.0472	-0.1934	-0.2412	-0.0361	0.3149	0.2236	0.0754	-0.0804	-0.0442	0.2967	0.0672	0.0919	5.7988	24.9928	14.1828
16	1.9523	0.3565	-3.8977	0.1273	-0.7928	7.9397	-0.2824	-0.4942	-0.1846	-0.0627	-0.252	-0.1094	0.5756	1.1061	0.5343	0.1286	0.0339	0.1374	0.4637	0.1097	0.2877	8.725	28.514	-1.5842
17	0.5456	0.2103	-0.3845	2.033	-0.7478	1.4772	-0.0428	-0.0686	0.0132	-0.1416	-0.025	-0.0566	0.1041	0.282	0.0678	0.1553	-0.0795	0.0178	0.1227	0.0042	0.1205	-1.5329	31.0781	-1.3151
18	3.5164	-1.2092	1.7366	0.4267	-0.1212	21.8274	-0.1285	0.36	0.2697	0.0566	-0.105	-0.0895	0.0679	0.0905	0.2335	0.3462	-0.2614	0.0214	0.215	0.0053	0.056	-8.414	27.1738	-19.5295
19	1.9236	1.5464	-0.4953	2.7739	0.0075	3.6894	-0.2856	0.3528	-0.0677	-0.2417	0.3361	0.0828	0.1701	0.1469	-0.0505	0.2926	-0.1629	0.0476	0.1362	-0.0366	0.0437	-8.7011	21.7018	-12.6407
20	4.0409	-0.2409	-0.6923	4.6495	0.2374	0.1332	-0.3319	0.514	-0.385	-0.1605	0.302	-0.1988	0.0866	-0.0814	0.03	0.3882	-0.1806	0.0385	0.1585	-0.1014	0.1064	-10.5879	14.8965	-15.1191

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 6
2	X-RAY DIFFRACTION	2	A	7 - 25
3	X-RAY DIFFRACTION	3	A	26 - 37
4	X-RAY DIFFRACTION	4	A	38 - 66
5	X-RAY DIFFRACTION	5	A	67 - 86
6	X-RAY DIFFRACTION	6	A	87 - 99
7	X-RAY DIFFRACTION	7	A	100 - 107
8	X-RAY DIFFRACTION	8	A	108 - 129
9	X-RAY DIFFRACTION	9	A	130 - 139
10	X-RAY DIFFRACTION	10	A	140 - 171
11	X-RAY DIFFRACTION	11	B	1 - 16
12	X-RAY DIFFRACTION	12	B	17 - 25
13	X-RAY DIFFRACTION	13	B	26 - 34
14	X-RAY DIFFRACTION	14	B	35 - 72
15	X-RAY DIFFRACTION	15	B	73 - 86
16	X-RAY DIFFRACTION	16	B	87 - 96
17	X-RAY DIFFRACTION	17	B	97 - 129
18	X-RAY DIFFRACTION	18	B	130 - 135
19	X-RAY DIFFRACTION	19	B	136 - 159
20	X-RAY DIFFRACTION	20	B	160 - 170

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Yorodumi