PDB-7w4b: Phloem lectin (PP2) structure -complex with Chitotrise

Basic information

• Entry: Database: PDB / ID: 7w4b
• Title: Phloem lectin (PP2) structure -complex with Chitotrise
• Components: 17 kDa phloem lectin
• Keywords: SUGAR BINDING PROTEIN / Chitin-binding protein / Phloem lectin
• Function / homology: Phloem protein 2-like / Phloem protein 2 / carbohydrate binding / triacetyl-beta-chitotriose / 17 kDa phloem lectin
• Biological species: Cucumis sativus (cucumber)
• Method: X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
• Authors: Sivaji, N. / Kishore, B.B. / Suguna, K. / Surolia, A.

Funding support

India, 1items

Organization	Grant number	Country
Department of Biotechnology (DBT, India)		India

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

History

Deposition	Nov 26, 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
Revision 2.0	May 22, 2024	Group: Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary Category: atom_site / atom_sites / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_branch_scheme / pdbx_contact_author / pdbx_molecule_features / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / reflns / software / struct_asym / struct_conf / struct_conn / struct_ncs_dom / struct_ncs_dom_lim / struct_ref / struct_ref_seq / struct_sheet_range Item: _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_end_seq_num / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.ls_wR_factor_R_free / _refine.ls_wR_factor_R_work / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_R_Free_selection_details / _refine.pdbx_average_fsc_free / _refine.pdbx_average_fsc_work / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.d_res_low / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _reflns.number_obs / _software.version / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id Description: Ligand geometry / Provider: author / Type: Coordinate replacement

Assembly

Deposited unit

A: 17 kDa phloem lectin

B: 17 kDa phloem lectin

C: 17 kDa phloem lectin

D: 17 kDa phloem lectin

E: 17 kDa phloem lectin

F: 17 kDa phloem lectin

G: 17 kDa phloem lectin

H: 17 kDa phloem lectin

I: 17 kDa phloem lectin

J: 17 kDa phloem lectin

K: 17 kDa phloem lectin

L: 17 kDa phloem lectin

hetero molecules

Summary:

• 215 kDa, 12 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	214,560	24
Polymers	207,029	12
Non-polymers	7,531	12
Water	0	0

1

Summary:

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

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	4500 Å2
ΔGint	3 kcal/mol
Surface area	12990 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	83.290, 92.410, 280.780
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P212121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	A
2	4	E
1	5	A
2	5	F
1	6	A
2	6	G
1	7	A
2	7	H
1	8	A
2	8	I
1	9	A
2	9	J
1	10	A
2	10	K
1	11	A
2	11	L
1	12	B
2	12	C
1	13	B
2	13	D
1	14	B
2	14	E
1	15	B
2	15	F
1	16	B
2	16	G
1	17	B
2	17	H
1	18	B
2	18	I
1	19	B
2	19	J
1	20	B
2	20	K
1	21	B
2	21	L
1	22	C
2	22	D
1	23	C
2	23	E
1	24	C
2	24	F
1	25	C
2	25	G
1	26	C
2	26	H
1	27	C
2	27	I
1	28	C
2	28	J
1	29	C
2	29	K
1	30	C
2	30	L
1	31	D
2	31	E
1	32	D
2	32	F
1	33	D
2	33	G
1	34	D
2	34	H
1	35	D
2	35	I
1	36	D
2	36	J
1	37	D
2	37	K
1	38	D
2	38	L
1	39	E
2	39	F
1	40	E
2	40	G
1	41	E
2	41	H
1	42	E
2	42	I
1	43	E
2	43	J
1	44	E
2	44	K
1	45	E
2	45	L
1	46	F
2	46	G
1	47	F
2	47	H
1	48	F
2	48	I
1	49	F
2	49	J
1	50	F
2	50	K
1	51	F
2	51	L
1	52	G
2	52	H
1	53	G
2	53	I
1	54	G
2	54	J
1	55	G
2	55	K
1	56	G
2	56	L
1	57	H
2	57	I
1	58	H
2	58	J
1	59	H
2	59	K
1	60	H
2	60	L
1	61	I
2	61	J
1	62	I
2	62	K
1	63	I
2	63	L
1	64	J
2	64	K
1	65	J
2	65	L
1	66	K
2	66	L

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 5 - 154 / Label seq-ID: 1 - 150

Dom-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	A	A
2	1	B	B
1	2	A	A
2	2	C	C
1	3	A	A
2	3	D	D
1	4	A	A
2	4	E	E
1	5	A	A
2	5	F	F
1	6	A	A
2	6	G	G
1	7	A	A
2	7	H	H
1	8	A	A
2	8	I	I
1	9	A	A
2	9	J	J
1	10	A	A
2	10	K	K
1	11	A	A
2	11	L	L
1	12	B	B
2	12	C	C
1	13	B	B
2	13	D	D
1	14	B	B
2	14	E	E
1	15	B	B
2	15	F	F
1	16	B	B
2	16	G	G
1	17	B	B
2	17	H	H
1	18	B	B
2	18	I	I
1	19	B	B
2	19	J	J
1	20	B	B
2	20	K	K
1	21	B	B
2	21	L	L
1	22	C	C
2	22	D	D
1	23	C	C
2	23	E	E
1	24	C	C
2	24	F	F
1	25	C	C
2	25	G	G
1	26	C	C
2	26	H	H
1	27	C	C
2	27	I	I
1	28	C	C
2	28	J	J
1	29	C	C
2	29	K	K
1	30	C	C
2	30	L	L
1	31	D	D
2	31	E	E
1	32	D	D
2	32	F	F
1	33	D	D
2	33	G	G
1	34	D	D
2	34	H	H
1	35	D	D
2	35	I	I
1	36	D	D
2	36	J	J
1	37	D	D
2	37	K	K
1	38	D	D
2	38	L	L
1	39	E	E
2	39	F	F
1	40	E	E
2	40	G	G
1	41	E	E
2	41	H	H
1	42	E	E
2	42	I	I
1	43	E	E
2	43	J	J
1	44	E	E
2	44	K	K
1	45	E	E
2	45	L	L
1	46	F	F
2	46	G	G
1	47	F	F
2	47	H	H
1	48	F	F
2	48	I	I
1	49	F	F
2	49	J	J
1	50	F	F
2	50	K	K
1	51	F	F
2	51	L	L
1	52	G	G
2	52	H	H
1	53	G	G
2	53	I	I
1	54	G	G
2	54	J	J
1	55	G	G
2	55	K	K
1	56	G	G
2	56	L	L
1	57	H	H
2	57	I	I
1	58	H	H
2	58	J	J
1	59	H	H
2	59	K	K
1	60	H	H
2	60	L	L
1	61	I	I
2	61	J	J
1	62	I	I
2	62	K	K
1	63	I	I
2	63	L	L
1	64	J	J
2	64	K	K
1	65	J	J
2	65	L	L
1	66	K	K
2	66	L	L

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66

Components

#1: Protein

A B C D E F G H I J K L
17 kDa phloem lectin

Details:

Mass: 17252.416 Da / Num. of mol.: 12
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

[M] [N] [O] [P] [Q] [R] [S] [T] [U] [V] [W] Y - [X]
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

Details:

Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 12 / Source method: obtained synthetically / Details: oligosaccharide / References: triacetyl-beta-chitotriose

Descriptor:

Descriptor	Type	Program
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1	WURCS	PDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}	LINUCS	PDB-CARE

• Has ligand of interest: Y

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 2.65 ų/Da / Density % sol: 53.59 %
• Crystal grow: Temperature: 295 K / Method: microbatch / pH: 7.2 ; Details: 0.1 M Imidazole pH 7.0, 20% w/v Polyethylene glycol 6,000

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: Jan 19, 2021
• Radiation: Monochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 1.5418 Å / Relative weight: 1
• Reflection: Resolution: 2.5→53.67 Å / Num. obs: 64194 / % possible obs: 89.3 % / Redundancy: 8.3 % / CC_1/2: 0.96 / R_merge(I) obs: 0.32 / Net I/σ(I): 5.1
• Reflection shell: Resolution: 2.5→2.64 Å / R_merge(I) obs: 0.79 / Num. unique obs: 89566 / CC_1/2: 0.88

Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
iMOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VWB

7vwb

Resolution: 2.5→51.61 Å / Cor.coef. F_o:F_c: 0.842 / Cor.coef. F_o:F_c free: 0.835 / SU B: 14.258 / SU ML: 0.308 / Cross valid method: THROUGHOUT / ESU R: 1.304 / ESU R Free: 0.377 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.29687	3483	5.1 %	RANDOM
Rwork	0.28209	-	-	-
obs	0.28287	64194	89.1 %	-

• 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: 17.147 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-0.09 Å2	0 Å2	-0 Å2
2-	-	0.05 Å2	-0 Å2
3-	-	-	0.04 Å2

Refinement step

Cycle: 1 / Resolution: 2.5→51.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14319	0	516	0	14835

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	15297
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	13848
X-RAY DIFFRACTION	r_angle_refined_deg	1.545	1.674	20798
X-RAY DIFFRACTION	r_angle_other_deg	1.166	1.624	31714
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.987	5	1728
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.607	21.357	833
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.84	15	2321
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.377	15	108
X-RAY DIFFRACTION	r_chiral_restr	0.057	0.2	2030
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	16926
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3958
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	1.399	1.76	6984
X-RAY DIFFRACTION	r_mcbond_other	1.399	1.76	6983
X-RAY DIFFRACTION	r_mcangle_it	2.353	2.633	8688
X-RAY DIFFRACTION	r_mcangle_other	2.353	2.633	8689
X-RAY DIFFRACTION	r_scbond_it	1.375	1.856	8313
X-RAY DIFFRACTION	r_scbond_other	1.375	1.856	8314
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.28	2.734	12111
X-RAY DIFFRACTION	r_long_range_B_refined	3.61	18.581	15572
X-RAY DIFFRACTION	r_long_range_B_other	3.61	18.582	15573
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	4677	0.04
1	2	B	4677	0.04
2	1	A	4679	0.04
2	2	C	4679	0.04
3	1	A	4652	0.04
3	2	D	4652	0.04
4	1	A	4718	0.02
4	2	E	4718	0.02
5	1	A	4674	0.03
5	2	F	4674	0.03
6	1	A	4707	0.02
6	2	G	4707	0.02
7	1	A	4674	0.04
7	2	H	4674	0.04
8	1	A	4691	0.04
8	2	I	4691	0.04
9	1	A	4676	0.03
9	2	J	4676	0.03
10	1	A	4677	0.04
10	2	K	4677	0.04
11	1	A	4683	0.03
11	2	L	4683	0.03
12	1	B	4688	0.01
12	2	C	4688	0.01
13	1	B	4653	0.03
13	2	D	4653	0.03
14	1	B	4668	0.03
14	2	E	4668	0.03
15	1	B	4679	0.02
15	2	F	4679	0.02
16	1	B	4661	0.04
16	2	G	4661	0.04
17	1	B	4668	0.03
17	2	H	4668	0.03
18	1	B	4690	0.03
18	2	I	4690	0.03
19	1	B	4681	0.02
19	2	J	4681	0.02
20	1	B	4699	0.02
20	2	K	4699	0.02
21	1	B	4682	0.03
21	2	L	4682	0.03
22	1	C	4649	0.04
22	2	D	4649	0.04
23	1	C	4674	0.04
23	2	E	4674	0.04
24	1	C	4665	0.02
24	2	F	4665	0.02
25	1	C	4664	0.04
25	2	G	4664	0.04
26	1	C	4666	0.03
26	2	H	4666	0.03
27	1	C	4691	0.04
27	2	I	4691	0.04
28	1	C	4670	0.02
28	2	J	4670	0.02
29	1	C	4704	0.02
29	2	K	4704	0.02
30	1	C	4666	0.03
30	2	L	4666	0.03
31	1	D	4646	0.04
31	2	E	4646	0.04
32	1	D	4654	0.03
32	2	F	4654	0.03
33	1	D	4654	0.04
33	2	G	4654	0.04
34	1	D	4670	0.03
34	2	H	4670	0.03
35	1	D	4671	0.03
35	2	I	4671	0.03
36	1	D	4651	0.03
36	2	J	4651	0.03
37	1	D	4652	0.04
37	2	K	4652	0.04
38	1	D	4658	0.03
38	2	L	4658	0.03
39	1	E	4658	0.03
39	2	F	4658	0.03
40	1	E	4707	0.02
40	2	G	4707	0.02
41	1	E	4663	0.04
41	2	H	4663	0.04
42	1	E	4675	0.04
42	2	I	4675	0.04
43	1	E	4667	0.03
43	2	J	4667	0.03
44	1	E	4673	0.03
44	2	K	4673	0.03
45	1	E	4665	0.04
45	2	L	4665	0.04
46	1	F	4654	0.03
46	2	G	4654	0.03
47	1	F	4680	0.03
47	2	H	4680	0.03
48	1	F	4668	0.03
48	2	I	4668	0.03
49	1	F	4684	0.01
49	2	J	4684	0.01
50	1	F	4675	0.02
50	2	K	4675	0.02
51	1	F	4699	0.03
51	2	L	4699	0.03
52	1	G	4657	0.04
52	2	H	4657	0.04
53	1	G	4690	0.04
53	2	I	4690	0.04
54	1	G	4661	0.03
54	2	J	4661	0.03
55	1	G	4662	0.04
55	2	K	4662	0.04
56	1	G	4656	0.04
56	2	L	4656	0.04
57	1	H	4667	0.04
57	2	I	4667	0.04
58	1	H	4672	0.03
58	2	J	4672	0.03
59	1	H	4669	0.03
59	2	K	4669	0.03
60	1	H	4684	0.03
60	2	L	4684	0.03
61	1	I	4677	0.03
61	2	J	4677	0.03
62	1	I	4693	0.03
62	2	K	4693	0.03
63	1	I	4671	0.04
63	2	L	4671	0.04
64	1	J	4683	0.02
64	2	K	4683	0.02
65	1	J	4694	0.03
65	2	L	4694	0.03
66	1	K	4680	0.03
66	2	L	4680	0.03

LS refinement shell

Resolution: 2.5→2.565 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.388	256	-
Rwork	0.354	4725	-
obs	-	-	90.15 %