PDB-7vwb: Phloem lectin (PP2) structure -complex with N-Acetyllactosamine (...

ID or keywords:

Entry

Database: PDB / ID: 7vwb

Title

Phloem lectin (PP2) structure -complex with N-Acetyllactosamine (LacNAc)

Components

phloem lectin

Keywords

SUGAR BINDING PROTEIN / Phloem lectin / chitin-binding lectin

Function / homology

Phloem protein 2-like /

Phloem protein 2 /

carbohydrate binding / N-acetyl-alpha-lactosamine / 17 kDa phloem lectin

Function and homology information

Biological species

Cucumis sativus (cucumber)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Sivaji, N. / Bobbili, K.B. / Suguna, K. / Surolia, A.

Funding support

India, 1items

Citation

Journal: Structure / Year: 2023
Title: Structure and interactions of the phloem lectin (phloem protein 2) Cus17 from Cucumis sativus.
Authors: Sivaji, N. / Bobbili, K.B. / Suguna, K. / Surolia, A.

History

Deposition	Nov 10, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 8, 2023	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7vwb.cif.gz	83.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7vwb.ent.gz	58.6 KB	Display	PDB format
PDBx/mmJSON format	7vwb.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/vw/7vwb ftp://data.pdbj.org/pub/pdb/validation_reports/vw/7vwb	HTTPS FTP

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Related structure data

Related structure data	7vs6SC 7vubC 7w4bC 7yaqC S: Starting model for refinement C: citing same article (ref.)
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

Deposited unit

A: phloem lectin

B: phloem lectin

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: native gel electrophoresis

Unit cell

Length a, b, c (Å)	37.690, 60.390, 82.980
Angle α, β, γ (deg.)	90.000, 99.130, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein

phloem lectin / PP2

Mass: 17651.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Cucumis sativus (cucumber) / Gene: Lec17-7 / Production host:

Escherichia coli (E. coli) / References: UniProt: Q8LK69

#2: Polysaccharide

beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose

Type: oligosaccharide

, Oligosaccharide

/ Class: Glycan component

/ Mass: 383.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: N-acetyl-alpha-lactosamine

Descriptor	Type	Program
DGalpb1-4DGlcpNAca1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a4-b1	WURCS	PDB2Glycan 1.1.0
[][<C8N1O3>]{[(1+1)][b-D-Galp]{}}	LINUCS	PDB-CARE

#3: Chemical

ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL /

Ethylene glycol

Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂

#4: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

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: 2.67 Å³/Da / Density % sol: 53.95 %
Crystal grow	Temperature: 295 K / Method: microbatch Details: 0.1 M MES monohydrate pH 6.0, 22% v/v Polyethylene glycol 400

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 12, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.9→30.19 Å / Num. obs: 28551 / % possible obs: 98 % / Redundancy: 4 % / CC_1/2: 0.97 / R_merge(I) obs: 0.13 / Net I/σ(I): 7
Reflection shell	Resolution: 1.9→2 Å / R_merge(I) obs: 0.18 / Num. unique obs: 4055 / CC_1/2: 0.88

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7VS6

7vs6

Resolution: 1.9→24.896 Å / Cor.coef. F_o:F_c: 0.906 / Cor.coef. F_o:F_c free: 0.89 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.153
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2485	1468	5.142 %
R_work	0.2185	27080	-
all	0.22	-	-
obs	-	28548	98.012 %

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: 13.985 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.64 Å²	0 Å²	-0.141 Å²
2-	-	-1.233 Å²	-0 Å²
3-	-	-	-0.344 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→24.896 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2423	0	56	240	2719

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	2555
X-RAY DIFFRACTION	r_bond_other_d	0.035	0.018	2256
X-RAY DIFFRACTION	r_angle_refined_deg	1.567	1.654	3487
X-RAY DIFFRACTION	r_angle_other_deg	2.35	1.609	5206
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.18	5	298
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.329	21.241	137
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.002	15	384
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.331	15	18
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	341
X-RAY DIFFRACTION	r_chiral_restr_other	0.021	0.2	6
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	2820
X-RAY DIFFRACTION	r_gen_planes_other	0.015	0.02	610
X-RAY DIFFRACTION	r_nbd_refined	0.183	0.2	437
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.225	0.2	2226
X-RAY DIFFRACTION	r_nbtor_refined	0.171	0.2	1185
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.075	0.2	1166
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.154	0.2	216
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.036	0.2	5
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.254	0.2	5
X-RAY DIFFRACTION	r_nbd_other	0.373	0.2	31
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.251	0.2	8
X-RAY DIFFRACTION	r_mcbond_it	1.192	1.414	1198
X-RAY DIFFRACTION	r_mcbond_other	1.189	1.413	1197
X-RAY DIFFRACTION	r_mcangle_it	1.892	2.116	1494
X-RAY DIFFRACTION	r_mcangle_other	1.893	2.116	1495
X-RAY DIFFRACTION	r_scbond_it	1.44	1.522	1357
X-RAY DIFFRACTION	r_scbond_other	1.437	1.522	1357
X-RAY DIFFRACTION	r_scangle_it	2.201	2.242	1993
X-RAY DIFFRACTION	r_scangle_other	2.202	2.243	1994
X-RAY DIFFRACTION	r_lrange_it	4.388	26.604	10751
X-RAY DIFFRACTION	r_lrange_other	4.382	26.545	10715
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.044	0.05	4970

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 (%)
1.9-1.949	0.335	129	0.237	1893	X-RAY DIFFRACTION	95.8748
1.949-2.003	0.262	110	0.225	1922	X-RAY DIFFRACTION	96.7619
2.003-2.061	0.258	86	0.218	1879	X-RAY DIFFRACTION	97.085
2.061-2.124	0.262	96	0.221	1818	X-RAY DIFFRACTION	97.3055
2.124-2.194	0.218	77	0.208	1813	X-RAY DIFFRACTION	97.6744
2.194-2.271	0.239	95	0.2	1682	X-RAY DIFFRACTION	97.5302
2.271-2.356	0.243	102	0.198	1684	X-RAY DIFFRACTION	97.9167
2.356-2.452	0.262	76	0.218	1589	X-RAY DIFFRACTION	98.1143
2.452-2.561	0.224	77	0.215	1547	X-RAY DIFFRACTION	98.3646
2.561-2.686	0.274	81	0.223	1512	X-RAY DIFFRACTION	98.8827
2.686-2.831	0.248	79	0.212	1377	X-RAY DIFFRACTION	98.7788
2.831-3.003	0.261	83	0.218	1332	X-RAY DIFFRACTION	99.0896
3.003-3.21	0.253	76	0.223	1260	X-RAY DIFFRACTION	98.8897
3.21-3.467	0.236	61	0.233	1178	X-RAY DIFFRACTION	99.5181
3.467-3.797	0.274	51	0.236	1105	X-RAY DIFFRACTION	99.3127
3.797-4.244	0.218	59	0.202	962	X-RAY DIFFRACTION	99.4158
4.244-4.898	0.2	36	0.195	889	X-RAY DIFFRACTION	99.0364
4.898-5.994	0.246	56	0.235	729	X-RAY DIFFRACTION	99.2415
5.994-8.454	0.245	26	0.259	587	X-RAY DIFFRACTION	99.3517
8.454-24	0.214	12	0.221	322	X-RAY DIFFRACTION	94.0845

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