PDB-7bsm: Mevo lectin complex with 2alpha-mannobiose

ID or keywords:

Entry

Database: PDB / ID: 7bsm

Title

Mevo lectin complex with 2alpha-mannobiose

Components

lectin

Keywords

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

Function / homology

Function and homology information

Jacalin-like lectin domain / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain superfamily / Mainly Beta
Similarity search - Domain/homology

Biological species

Methanococcus voltae (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 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 31, 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	7bsm.cif.gz	371.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7bsm.ent.gz	302.5 KB	Display	PDB format
PDBx/mmJSON format	7bsm.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/7bsm ftp://data.pdbj.org/pub/pdb/validation_reports/bs/7bsm	HTTPS FTP

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Related structure data

Related structure data	7bsbSC 7bsnC 7bt8C 7bt9C 7bthC 7btlC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7bsn-1 7bsn-2 7bt8-d 7bt9-2 7bsb-1 7bt9-1 7btl-d 7bsb-2 7bth-d 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
Related items in Molecule of the Month	#169 - Jan 2014 HIV Envelope Glycoprotein similarity (1) #170 - Feb 2014 Broadly Neutralizing Antibodies similarity (1) #247 - Jul 2020 Myelin-associated Glycoprotein similarity (1) #74 - Feb 2006 alpha-Amylase similarity (1) #83 - Nov 2006 Fibrin similarity (1)

Deposited unit

A: lectin

B: lectin

C: lectin

D: lectin

E: lectin

F: lectin

G: lectin

H: lectin

I: lectin

J: lectin

K: lectin

L: lectin

M: lectin

N: lectin

hetero molecules

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

1

A: lectin

B: lectin

C: lectin

D: lectin

E: lectin

F: lectin

G: lectin

hetero molecules

defined by author
Evidence: gel filtration, Protein 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
113 kDa, 7 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	170.359, 170.359, 192.499
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: Polysaccharide

alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose / 2alpha-alpha-mannobiose

Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 2alpha-alpha-mannobiose

#3: Sugar

ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose

Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C₆H₁₂O₆

#4: Chemical

ChemComp-ALA / ALANINE

Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₇NO₂

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: 2.85 Å³/Da / Density % sol: 56.9 %
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: 5.8-7.8

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9767 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 11, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9767 Å / Relative weight: 1
Reflection	Resolution: 2.8→96.25 Å / Num. obs: 70202 / % possible obs: 100 % / Redundancy: 13.2 % / CC_1/2: 0.99 / R_merge(I) obs: 0.22 / Net I/σ(I): 9
Reflection shell	Resolution: 2.8→2.95 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 10083 / CC_1/2: 0.73 / % possible all: 100

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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: 7BSB

7bsb

Resolution: 2.8→96.25 Å / Cor.coef. F_o:F_c: 0.929 / Cor.coef. F_o:F_c free: 0.92 / Cross valid method: THROUGHOUT / ESU R: 0.929 / ESU R Free: 0.35
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2604	3494	4.983 %
R_work	0.2271	-	-
all	0.229	-	-
obs	-	70117	99.987 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 53.106 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.908 Å²	0 Å²	-0 Å²
2-	-	-2.908 Å²	-0 Å²
3-	-	-	5.817 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→96.25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14630	0	224	0	14854

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.013	15124
X-RAY DIFFRACTION	r_bond_other_d	0.037	0.018	13862
X-RAY DIFFRACTION	r_angle_refined_deg	1.89	1.659	20454
X-RAY DIFFRACTION	r_angle_other_deg	2.499	1.606	32184
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.685	5	1944
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.968	24.385	602
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.779	15	2474
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.514	15	26
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	2182
X-RAY DIFFRACTION	r_chiral_restr_other	0.022	0.2	19
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	16788
X-RAY DIFFRACTION	r_gen_planes_other	0.016	0.02	3010
X-RAY DIFFRACTION	r_nbd_refined	0.191	0.2	2347
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.227	0.2	12642
X-RAY DIFFRACTION	r_nbtor_refined	0.172	0.2	7277
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	6873
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.175	0.2	165
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.075	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.211	0.2	19
X-RAY DIFFRACTION	r_nbd_other	0.287	0.2	67
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.213	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	7.053	5.538	7821
X-RAY DIFFRACTION	r_mcbond_other	7.054	5.538	7820
X-RAY DIFFRACTION	r_mcangle_it	9.823	8.319	9750
X-RAY DIFFRACTION	r_mcangle_other	9.822	8.319	9751
X-RAY DIFFRACTION	r_scbond_it	7.926	6.089	7303
X-RAY DIFFRACTION	r_scbond_other	7.926	6.089	7304
X-RAY DIFFRACTION	r_scangle_it	10.958	8.94	10704
X-RAY DIFFRACTION	r_scangle_other	10.959	8.94	10705
X-RAY DIFFRACTION	r_lrange_it	12.869	64.806	15367
X-RAY DIFFRACTION	r_lrange_other	12.872	64.805	15367
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.084	0.05	3911
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.088	0.05	4000
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.099	0.05	4037
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.093	0.05	4077
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.093	0.05	4004
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.088	0.05	3976
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.072	0.05	4174
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.098	0.05	3941
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.096	0.05	3954
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.089	0.05	4039
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.086	0.05	4072
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.08	0.05	4035
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.083	0.05	4024
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.071	0.05	3829
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.092	0.05	3853
X-RAY DIFFRACTION	r_ncsr_local_group_16	0.077	0.05	3923
X-RAY DIFFRACTION	r_ncsr_local_group_17	0.076	0.05	3879
X-RAY DIFFRACTION	r_ncsr_local_group_18	0.081	0.05	3842
X-RAY DIFFRACTION	r_ncsr_local_group_19	0.085	0.05	3926
X-RAY DIFFRACTION	r_ncsr_local_group_20	0.091	0.05	3912
X-RAY DIFFRACTION	r_ncsr_local_group_21	0.096	0.05	3736
X-RAY DIFFRACTION	r_ncsr_local_group_22	0.087	0.05	3876
X-RAY DIFFRACTION	r_ncsr_local_group_23	0.083	0.05	3898
X-RAY DIFFRACTION	r_ncsr_local_group_24	0.074	0.05	3914
X-RAY DIFFRACTION	r_ncsr_local_group_25	0.074	0.05	3872
X-RAY DIFFRACTION	r_ncsr_local_group_26	0.083	0.05	3955
X-RAY DIFFRACTION	r_ncsr_local_group_27	0.074	0.05	3994
X-RAY DIFFRACTION	r_ncsr_local_group_28	0.078	0.05	3955
X-RAY DIFFRACTION	r_ncsr_local_group_29	0.085	0.05	3875
X-RAY DIFFRACTION	r_ncsr_local_group_30	0.08	0.05	4022
X-RAY DIFFRACTION	r_ncsr_local_group_31	0.098	0.05	3848
X-RAY DIFFRACTION	r_ncsr_local_group_32	0.093	0.05	3977
X-RAY DIFFRACTION	r_ncsr_local_group_33	0.083	0.05	3946
X-RAY DIFFRACTION	r_ncsr_local_group_34	0.08	0.05	3971
X-RAY DIFFRACTION	r_ncsr_local_group_35	0.074	0.05	3948
X-RAY DIFFRACTION	r_ncsr_local_group_36	0.07	0.05	3969
X-RAY DIFFRACTION	r_ncsr_local_group_37	0.092	0.05	4037
X-RAY DIFFRACTION	r_ncsr_local_group_38	0.097	0.05	3986
X-RAY DIFFRACTION	r_ncsr_local_group_39	0.097	0.05	3918
X-RAY DIFFRACTION	r_ncsr_local_group_40	0.096	0.05	4060
X-RAY DIFFRACTION	r_ncsr_local_group_41	0.115	0.05	3862
X-RAY DIFFRACTION	r_ncsr_local_group_42	0.118	0.05	3843
X-RAY DIFFRACTION	r_ncsr_local_group_43	0.089	0.05	4036
X-RAY DIFFRACTION	r_ncsr_local_group_44	0.101	0.05	4004
X-RAY DIFFRACTION	r_ncsr_local_group_45	0.093	0.05	3994
X-RAY DIFFRACTION	r_ncsr_local_group_46	0.095	0.05	3970
X-RAY DIFFRACTION	r_ncsr_local_group_47	0.078	0.05	4032
X-RAY DIFFRACTION	r_ncsr_local_group_48	0.074	0.05	3983
X-RAY DIFFRACTION	r_ncsr_local_group_49	0.08	0.05	4108
X-RAY DIFFRACTION	r_ncsr_local_group_50	0.094	0.05	3973
X-RAY DIFFRACTION	r_ncsr_local_group_51	0.106	0.05	3889
X-RAY DIFFRACTION	r_ncsr_local_group_52	0.092	0.05	4020
X-RAY DIFFRACTION	r_ncsr_local_group_53	0.076	0.05	4098
X-RAY DIFFRACTION	r_ncsr_local_group_54	0.074	0.05	4054
X-RAY DIFFRACTION	r_ncsr_local_group_55	0.071	0.05	4031
X-RAY DIFFRACTION	r_ncsr_local_group_56	0.086	0.05	3950
X-RAY DIFFRACTION	r_ncsr_local_group_57	0.081	0.05	4053
X-RAY DIFFRACTION	r_ncsr_local_group_58	0.1	0.05	3885
X-RAY DIFFRACTION	r_ncsr_local_group_59	0.098	0.05	3866
X-RAY DIFFRACTION	r_ncsr_local_group_60	0.085	0.05	3999
X-RAY DIFFRACTION	r_ncsr_local_group_61	0.096	0.05	3998
X-RAY DIFFRACTION	r_ncsr_local_group_62	0.078	0.05	4015
X-RAY DIFFRACTION	r_ncsr_local_group_63	0.083	0.05	3980
X-RAY DIFFRACTION	r_ncsr_local_group_64	0.078	0.05	4021
X-RAY DIFFRACTION	r_ncsr_local_group_65	0.1	0.05	3859
X-RAY DIFFRACTION	r_ncsr_local_group_66	0.11	0.05	3767
X-RAY DIFFRACTION	r_ncsr_local_group_67	0.087	0.05	3938
X-RAY DIFFRACTION	r_ncsr_local_group_68	0.087	0.05	3964
X-RAY DIFFRACTION	r_ncsr_local_group_69	0.077	0.05	3948
X-RAY DIFFRACTION	r_ncsr_local_group_70	0.079	0.05	3951
X-RAY DIFFRACTION	r_ncsr_local_group_71	0.101	0.05	3968
X-RAY DIFFRACTION	r_ncsr_local_group_72	0.098	0.05	3945
X-RAY DIFFRACTION	r_ncsr_local_group_73	0.083	0.05	4069
X-RAY DIFFRACTION	r_ncsr_local_group_74	0.084	0.05	4084
X-RAY DIFFRACTION	r_ncsr_local_group_75	0.078	0.05	4067
X-RAY DIFFRACTION	r_ncsr_local_group_76	0.08	0.05	4045
X-RAY DIFFRACTION	r_ncsr_local_group_77	0.108	0.05	3789
X-RAY DIFFRACTION	r_ncsr_local_group_78	0.107	0.05	3887
X-RAY DIFFRACTION	r_ncsr_local_group_79	0.084	0.05	3953
X-RAY DIFFRACTION	r_ncsr_local_group_80	0.087	0.05	3947
X-RAY DIFFRACTION	r_ncsr_local_group_81	0.091	0.05	3934
X-RAY DIFFRACTION	r_ncsr_local_group_82	0.103	0.05	3857
X-RAY DIFFRACTION	r_ncsr_local_group_83	0.106	0.05	3878
X-RAY DIFFRACTION	r_ncsr_local_group_84	0.097	0.05	3854
X-RAY DIFFRACTION	r_ncsr_local_group_85	0.1	0.05	3873
X-RAY DIFFRACTION	r_ncsr_local_group_86	0.093	0.05	4021
X-RAY DIFFRACTION	r_ncsr_local_group_87	0.078	0.05	3996
X-RAY DIFFRACTION	r_ncsr_local_group_88	0.087	0.05	3987
X-RAY DIFFRACTION	r_ncsr_local_group_89	0.079	0.05	4061
X-RAY DIFFRACTION	r_ncsr_local_group_90	0.075	0.05	4055
X-RAY DIFFRACTION	r_ncsr_local_group_91	0.067	0.05	4058

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 (%)
2.8-2.873	0.369	242	0.372	4850	X-RAY DIFFRACTION	100
2.873-2.951	0.379	218	0.352	4766	X-RAY DIFFRACTION	99.9799
2.951-3.037	0.351	271	0.33	4573	X-RAY DIFFRACTION	100
3.037-3.13	0.363	212	0.292	4513	X-RAY DIFFRACTION	100
3.13-3.233	0.322	244	0.275	4334	X-RAY DIFFRACTION	100
3.233-3.346	0.312	193	0.251	4249	X-RAY DIFFRACTION	99.9775
3.346-3.473	0.284	229	0.23	4028	X-RAY DIFFRACTION	99.9765
3.473-3.614	0.281	212	0.231	3906	X-RAY DIFFRACTION	99.9515
3.614-3.775	0.246	227	0.223	3743	X-RAY DIFFRACTION	100
3.775-3.959	0.233	200	0.224	3604	X-RAY DIFFRACTION	100
3.959-4.173	0.241	173	0.197	3438	X-RAY DIFFRACTION	100
4.173-4.426	0.191	173	0.172	3241	X-RAY DIFFRACTION	100
4.426-4.731	0.189	154	0.155	3104	X-RAY DIFFRACTION	100
4.731-5.109	0.208	170	0.165	2840	X-RAY DIFFRACTION	100
5.109-5.596	0.252	123	0.191	2678	X-RAY DIFFRACTION	100
5.596-6.255	0.273	116	0.213	2418	X-RAY DIFFRACTION	100
6.255-7.22	0.25	107	0.215	2168	X-RAY DIFFRACTION	100
7.22-8.835	0.263	93	0.215	1845	X-RAY DIFFRACTION	100
8.835-12.465	0.227	76	0.237	1460	X-RAY DIFFRACTION	100
12.465-13.7	0.324	61	0.379	865	X-RAY DIFFRACTION	99.5699

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