PDB-7bsb: Mevo lectin- Native form-2

ID or keywords:

Entry

Database: PDB / ID: 7bsb

Title

Mevo lectin- Native form-2

Components

lectin

Keywords

SUGAR BINDING PROTEIN / beta-prism I fold lectin / Archeal lectin / heptamer / ring shape structure

Function / homology

Jacalin-like lectin domain superfamily / Jacalin-type lectin domain-containing protein

Function and homology information

Biological species

Methanococcus voltae (archaea)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.45 Å

Authors

Sivaji, N. / Suguna, K. / Surolia, A. / Vijayan, M.

Funding support

India, 1items

Citation

Journal: Glycobiology / Year: 2021
Title: Structural and related studies on Mevo lectin from Methanococcus voltae A3: the first thorough characterization of an archeal lectin and its interactions.
Authors: Sivaji, N. / Suguna, K. / Surolia, A. / Vijayan, M.

History

Deposition	Mar 30, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Feb 3, 2021	Provider: repository / Type: Initial release
Revision 1.1	Apr 21, 2021	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2	Nov 29, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7bsb.cif.gz	373.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7bsb.ent.gz	304.8 KB	Display	PDB format
PDBx/mmJSON format	7bsb.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/bs/7bsb ftp://data.pdbj.org/pub/pdb/validation_reports/bs/7bsb	HTTPS FTP

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Related structure data

Related structure data	7bsmC 7bsnC 7bt8C 7bt9C 7bthC 7btlC 4znoS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7bt9-1 7bsm-1 7bt8-d 7bsn-2 7bt9-2 7bth-d 7bsn-1 7btl-d 7bsm-2 7ded-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

B: lectin

G: lectin

A: lectin

D: lectin

E: lectin

F: lectin

C: lectin

H: lectin

I: lectin

J: lectin

K: lectin

L: lectin

M: lectin

N: lectin

hetero molecules

223 kDa, 14 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

B: lectin

G: lectin

A: lectin

D: lectin

E: lectin

F: lectin

C: lectin

hetero molecules

defined by author
Evidence: gel filtration, In analytical gel filtration experiments, molecule elutes as heptamer
112 kDa, 7 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

H: lectin

I: lectin

J: lectin

K: lectin

L: lectin

M: lectin

N: lectin

hetero molecules

defined by author
111 kDa, 7 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	169.450, 169.450, 192.230
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	lectin / Mass: 15783.812 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanococcus voltae (strain ATCC BAA-1334 / A3) (archaea) Strain: ATCC BAA-1334 / A3 / Gene: Mvol_0737 / Production host: Escherichia coli (E. coli) / References: UniProt: D7DTD6
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.82 Å³/Da / Density % sol: 56.35 %
Crystal grow	Temperature: 296 K / Method: microbatch Details: 6%(v/v) Tacsimate pH 6.0, 0.1 M MES monohydrate pH 6.0, 25%(w/v) polyethylene glycol 4000 PH range: 5.8-7.6

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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: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 10, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.45→96.12 Å / Num. obs: 102790 / % possible obs: 99.9 % / Redundancy: 12.7 % / CC_1/2: 0.998 / R_merge(I) obs: 0.14 / Net I/σ(I): 11.8
Reflection shell	Resolution: 2.45→2.58 Å / Redundancy: 10 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 14786 / CC_1/2: 0.828 / % possible all: 99.8

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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: 4ZNO

4zno

Resolution: 2.45→70.599 Å / Cor.coef. F_o:F_c: 0.939 / Cor.coef. F_o:F_c free: 0.916 / WR_factor R_free: 0.27 / WR_factor R_work: 0.231 / Average fsc free: 0.8751 / Average fsc work: 0.8953 / Cross valid method: FREE R-VALUE / ESU R: 0.37 / ESU R Free: 0.266
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2704	5134	5.028 %
R_work	0.2311	96967	-
all	0.233	-	-
obs	-	102101	99.312 %

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: 47.684 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.192 Å²	0 Å²	0 Å²
2-	-	-3.192 Å²	0 Å²
3-	-	-	6.385 Å²

Refinement step

Cycle: LAST / Resolution: 2.45→70.599 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14676	0	110	281	15067

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.013	15022
X-RAY DIFFRACTION	r_bond_other_d	0.036	0.017	13977
X-RAY DIFFRACTION	r_angle_refined_deg	1.717	1.638	20219
X-RAY DIFFRACTION	r_angle_other_deg	2.422	1.583	32459
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.303	5	1922
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.937	24.446	623
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.398	15	2561
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.26	15	28
X-RAY DIFFRACTION	r_chiral_restr	0.074	0.2	2071
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	16714
X-RAY DIFFRACTION	r_gen_planes_other	0.019	0.02	3000
X-RAY DIFFRACTION	r_nbd_refined	0.17	0.2	2025
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.215	0.2	12703
X-RAY DIFFRACTION	r_nbtor_refined	0.162	0.2	7083
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.077	0.2	6803
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.153	0.2	403
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.094	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.203	0.2	21
X-RAY DIFFRACTION	r_nbd_other	0.273	0.2	115
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.196	0.2	10
X-RAY DIFFRACTION	r_mcbond_it	6.463	4.893	7745
X-RAY DIFFRACTION	r_mcbond_other	6.462	4.893	7744
X-RAY DIFFRACTION	r_mcangle_it	8.583	7.335	9648
X-RAY DIFFRACTION	r_mcangle_other	8.583	7.335	9649
X-RAY DIFFRACTION	r_scbond_it	7.126	5.395	7277
X-RAY DIFFRACTION	r_scbond_other	7.125	5.395	7278
X-RAY DIFFRACTION	r_scangle_it	9.612	7.862	10571
X-RAY DIFFRACTION	r_scangle_other	9.611	7.862	10572
X-RAY DIFFRACTION	r_lrange_it	12.027	94.754	61407
X-RAY DIFFRACTION	r_lrange_other	12.029	94.772	61370
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.062	0.05	4100
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.062	0.05	4228
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.072	0.05	4234
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.067	0.05	4190
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.055	0.05	4218
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.064	0.05	4227
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.056	0.05	4200
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.057	0.05	3958
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.048	0.05	4308
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.072	0.05	4247
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.062	0.05	4198
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.068	0.05	4225
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.061	0.05	4131
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.069	0.05	4020
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.06	0.05	4047
X-RAY DIFFRACTION	r_ncsr_local_group_16	0.065	0.05	4082
X-RAY DIFFRACTION	r_ncsr_local_group_17	0.05	0.05	4085
X-RAY DIFFRACTION	r_ncsr_local_group_18	0.063	0.05	4050
X-RAY DIFFRACTION	r_ncsr_local_group_19	0.067	0.05	4001
X-RAY DIFFRACTION	r_ncsr_local_group_20	0.07	0.05	3980
X-RAY DIFFRACTION	r_ncsr_local_group_21	0.067	0.05	4076
X-RAY DIFFRACTION	r_ncsr_local_group_22	0.06	0.05	4074
X-RAY DIFFRACTION	r_ncsr_local_group_23	0.061	0.05	4075
X-RAY DIFFRACTION	r_ncsr_local_group_24	0.066	0.05	4030
X-RAY DIFFRACTION	r_ncsr_local_group_25	0.055	0.05	4042
X-RAY DIFFRACTION	r_ncsr_local_group_26	0.064	0.05	4239
X-RAY DIFFRACTION	r_ncsr_local_group_27	0.06	0.05	4179
X-RAY DIFFRACTION	r_ncsr_local_group_28	0.048	0.05	4210
X-RAY DIFFRACTION	r_ncsr_local_group_29	0.056	0.05	4221
X-RAY DIFFRACTION	r_ncsr_local_group_30	0.054	0.05	4196
X-RAY DIFFRACTION	r_ncsr_local_group_31	0.05	0.05	4003
X-RAY DIFFRACTION	r_ncsr_local_group_32	0.066	0.05	4239
X-RAY DIFFRACTION	r_ncsr_local_group_33	0.07	0.05	4244
X-RAY DIFFRACTION	r_ncsr_local_group_34	0.059	0.05	4173
X-RAY DIFFRACTION	r_ncsr_local_group_35	0.051	0.05	4263
X-RAY DIFFRACTION	r_ncsr_local_group_36	0.056	0.05	4127
X-RAY DIFFRACTION	r_ncsr_local_group_37	0.061	0.05	4241
X-RAY DIFFRACTION	r_ncsr_local_group_38	0.04	0.05	4253
X-RAY DIFFRACTION	r_ncsr_local_group_39	0.056	0.05	4246
X-RAY DIFFRACTION	r_ncsr_local_group_40	0.067	0.05	4157
X-RAY DIFFRACTION	r_ncsr_local_group_41	0.064	0.05	3960
X-RAY DIFFRACTION	r_ncsr_local_group_42	0.081	0.05	4217
X-RAY DIFFRACTION	r_ncsr_local_group_43	0.062	0.05	4292
X-RAY DIFFRACTION	r_ncsr_local_group_44	0.059	0.05	4204
X-RAY DIFFRACTION	r_ncsr_local_group_45	0.061	0.05	4256
X-RAY DIFFRACTION	r_ncsr_local_group_46	0.04	0.05	4216
X-RAY DIFFRACTION	r_ncsr_local_group_47	0.04	0.05	4240
X-RAY DIFFRACTION	r_ncsr_local_group_48	0.054	0.05	4219
X-RAY DIFFRACTION	r_ncsr_local_group_49	0.064	0.05	4116
X-RAY DIFFRACTION	r_ncsr_local_group_50	0.061	0.05	3979
X-RAY DIFFRACTION	r_ncsr_local_group_51	0.069	0.05	4183
X-RAY DIFFRACTION	r_ncsr_local_group_52	0.062	0.05	4238
X-RAY DIFFRACTION	r_ncsr_local_group_53	0.061	0.05	4205
X-RAY DIFFRACTION	r_ncsr_local_group_54	0.046	0.05	4240
X-RAY DIFFRACTION	r_ncsr_local_group_55	0.046	0.05	4178
X-RAY DIFFRACTION	r_ncsr_local_group_56	0.037	0.05	4242
X-RAY DIFFRACTION	r_ncsr_local_group_57	0.054	0.05	4140
X-RAY DIFFRACTION	r_ncsr_local_group_58	0.06	0.05	3966
X-RAY DIFFRACTION	r_ncsr_local_group_59	0.062	0.05	4219
X-RAY DIFFRACTION	r_ncsr_local_group_60	0.042	0.05	4269
X-RAY DIFFRACTION	r_ncsr_local_group_61	0.057	0.05	4232
X-RAY DIFFRACTION	r_ncsr_local_group_62	0.038	0.05	4253
X-RAY DIFFRACTION	r_ncsr_local_group_63	0.036	0.05	4192
X-RAY DIFFRACTION	r_ncsr_local_group_64	0.055	0.05	4182
X-RAY DIFFRACTION	r_ncsr_local_group_65	0.067	0.05	3944
X-RAY DIFFRACTION	r_ncsr_local_group_66	0.074	0.05	4229
X-RAY DIFFRACTION	r_ncsr_local_group_67	0.062	0.05	4279
X-RAY DIFFRACTION	r_ncsr_local_group_68	0.064	0.05	4200
X-RAY DIFFRACTION	r_ncsr_local_group_69	0.055	0.05	4235
X-RAY DIFFRACTION	r_ncsr_local_group_70	0.045	0.05	4174
X-RAY DIFFRACTION	r_ncsr_local_group_71	0.059	0.05	3917
X-RAY DIFFRACTION	r_ncsr_local_group_72	0.065	0.05	4210
X-RAY DIFFRACTION	r_ncsr_local_group_73	0.071	0.05	4163
X-RAY DIFFRACTION	r_ncsr_local_group_74	0.056	0.05	4140
X-RAY DIFFRACTION	r_ncsr_local_group_75	0.063	0.05	4137
X-RAY DIFFRACTION	r_ncsr_local_group_76	0.058	0.05	4067
X-RAY DIFFRACTION	r_ncsr_local_group_77	0.064	0.05	3963
X-RAY DIFFRACTION	r_ncsr_local_group_78	0.064	0.05	3965
X-RAY DIFFRACTION	r_ncsr_local_group_79	0.057	0.05	3983
X-RAY DIFFRACTION	r_ncsr_local_group_80	0.057	0.05	3990
X-RAY DIFFRACTION	r_ncsr_local_group_81	0.059	0.05	3932
X-RAY DIFFRACTION	r_ncsr_local_group_82	0.08	0.05	4245
X-RAY DIFFRACTION	r_ncsr_local_group_83	0.067	0.05	4201
X-RAY DIFFRACTION	r_ncsr_local_group_84	0.068	0.05	4214
X-RAY DIFFRACTION	r_ncsr_local_group_85	0.067	0.05	4123
X-RAY DIFFRACTION	r_ncsr_local_group_86	0.065	0.05	4211
X-RAY DIFFRACTION	r_ncsr_local_group_87	0.063	0.05	4271
X-RAY DIFFRACTION	r_ncsr_local_group_88	0.046	0.05	4203
X-RAY DIFFRACTION	r_ncsr_local_group_89	0.066	0.05	4191
X-RAY DIFFRACTION	r_ncsr_local_group_90	0.056	0.05	4155
X-RAY DIFFRACTION	r_ncsr_local_group_91	0.046	0.05	4154

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 (%)
2.45-2.514	0.349	372	0.326	7104	X-RAY DIFFRACTION	99.5473
2.514-2.582	0.335	388	0.314	6895	X-RAY DIFFRACTION	99.6306
2.582-2.657	0.391	367	0.316	6731	X-RAY DIFFRACTION	99.691
2.657-2.739	0.359	326	0.289	6569	X-RAY DIFFRACTION	99.7541
2.739-2.829	0.349	338	0.276	6370	X-RAY DIFFRACTION	99.7027
2.829-2.928	0.334	324	0.271	6158	X-RAY DIFFRACTION	99.8152
2.928-3.039	0.312	297	0.257	5966	X-RAY DIFFRACTION	99.6341
3.039-3.163	0.305	310	0.24	5733	X-RAY DIFFRACTION	99.6866
3.163-3.303	0.295	279	0.244	5458	X-RAY DIFFRACTION	99.2046
3.303-3.464	0.266	286	0.226	5233	X-RAY DIFFRACTION	98.9955
3.464-3.651	0.27	275	0.241	4965	X-RAY DIFFRACTION	98.8493
3.651-3.873	0.258	224	0.221	4733	X-RAY DIFFRACTION	98.3922
3.873-4.14	0.266	259	0.223	4410	X-RAY DIFFRACTION	98.3776
4.14-4.471	0.205	211	0.181	4139	X-RAY DIFFRACTION	98.3718
4.471-4.897	0.199	199	0.163	3839	X-RAY DIFFRACTION	98.9706
4.897-5.474	0.211	199	0.181	3510	X-RAY DIFFRACTION	99.0387
5.474-6.319	0.289	150	0.216	3119	X-RAY DIFFRACTION	99.3315
6.319-7.735	0.221	144	0.213	2679	X-RAY DIFFRACTION	99.2965
7.735-10.918	0.229	106	0.203	2112	X-RAY DIFFRACTION	99.5065
10.918-12.7	0.258	80	0.302	1244	X-RAY DIFFRACTION	99.3994

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Yorodumi