PDB-7bth: Mevo lectin- Native form-1

ID or keywords:

Entry

Database: PDB / ID: 7bth

Title

Mevo lectin- Native form-1

Components

lectin

Keywords

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

Function / homology

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 / Jacalin-type lectin domain-containing protein

Function and homology information

Biological species

Methanococcus voltae (archaea)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.6 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	Apr 1, 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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PDBx/mmCIF format	7bth.cif.gz	343 KB	Display	PDBx/mmCIF format
PDB format	pdb7bth.ent.gz	278 KB	Display	PDB format
PDBx/mmJSON format	7bth.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7bth_validation.pdf.gz	790.2 KB	Display	wwPDB validaton report
Full document	7bth_full_validation.pdf.gz	804.7 KB	Display
Data in XML	7bth_validation.xml.gz	34 KB	Display
Data in CIF	7bth_validation.cif.gz	46.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bt/7bth ftp://data.pdbj.org/pub/pdb/validation_reports/bt/7bth	HTTPS FTP

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Related structure data

Related structure data	7bsbC 7bsmC 7bsnC 7bt8C 7bt9C 7btlC 4znoS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7bsb-2 7bsb-1 7bt9-1 7bsm-1 7bt9-2 7bsn-2 7bt8-d 7bsn-1 7btl-d 7bsm-2 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

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration, Protein elutes as heptamer

Unit cell

Length a, b, c (Å)	94.610, 168.220, 169.020
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	lectin Mass: 15783.812 Da / Num. of mol.: 7 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 Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.74 Å³/Da / Density % sol: 55.22 %
Crystal grow	Temperature: 296 K / Method: microbatch / pH: 7 Details: 2.0 M ammonium citrate tribasic, 0.1 M bis tris propane pH 7.0

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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: 1.54 Å
Detector	Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 5, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 2.6→59.7 Å / Num. obs: 41843 / % possible obs: 100 % / Redundancy: 9.5 % / CC_1/2: 0.99 / R_merge(I) obs: 0.22 / Net I/σ(I): 7.9
Reflection shell	Resolution: 2.6→2.74 Å / Redundancy: 14.7 % / Mean I/σ(I) obs: 2 / Num. unique obs: 6030 / CC_1/2: 0.85 / % 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: 4ZNO

4zno

Resolution: 2.6→59.687 Å / Cor.coef. F_o:F_c: 0.898 / Cor.coef. F_o:F_c free: 0.889 / WR_factor R_free: 0.295 / WR_factor R_work: 0.279 / SU B: 44.401 / SU ML: 0.398 / Average fsc free: 0.8214 / Average fsc work: 0.8346 / Cross valid method: THROUGHOUT / ESU R: 0.622 / ESU R Free: 0.343
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.3064	2092	5.011 %
R_work	0.2951	39653	-
all	0.296	-	-
obs	-	41745	99.828 %

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: 58.909 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.194 Å²	0 Å²	0 Å²
2-	-	-2.59 Å²	0 Å²
3-	-	-	0.396 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→59.687 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7050	0	6	56	7112

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.013	7172
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	6639
X-RAY DIFFRACTION	r_angle_refined_deg	1.781	1.637	9678
X-RAY DIFFRACTION	r_angle_other_deg	1.291	1.583	15375
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	9.07	5	932
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.209	24.201	288
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.864	15	1184
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	10.241	15	14
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	1009
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	8038
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1444
X-RAY DIFFRACTION	r_nbd_refined	0.193	0.2	1096
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.187	0.2	6230
X-RAY DIFFRACTION	r_nbtor_refined	0.172	0.2	3411
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	3482
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.134	0.2	105
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.368	0.2	14
X-RAY DIFFRACTION	r_nbd_other	0.242	0.2	44
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.47	0.2	2
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.021	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	0.515	1.137	3773
X-RAY DIFFRACTION	r_mcbond_other	0.515	1.137	3772
X-RAY DIFFRACTION	r_mcangle_it	0.885	1.704	4690
X-RAY DIFFRACTION	r_mcangle_other	0.885	1.704	4691
X-RAY DIFFRACTION	r_scbond_it	0.545	1.151	3398
X-RAY DIFFRACTION	r_scbond_other	0.545	1.151	3399
X-RAY DIFFRACTION	r_scangle_it	0.846	1.716	4988
X-RAY DIFFRACTION	r_scangle_other	0.846	1.716	4988
X-RAY DIFFRACTION	r_lrange_it	3.304	21.569	28828
X-RAY DIFFRACTION	r_lrange_other	3.283	21.561	28825
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.052	0.05	3922
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.071	0.05	3790
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.07	0.05	3846
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.061	0.05	3964
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.067	0.05	3772
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.044	0.05	3977
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.073	0.05	3794
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.082	0.05	3849
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.071	0.05	3925
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.076	0.05	3722
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.069	0.05	3951
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.074	0.05	3774
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.079	0.05	3786
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.057	0.05	3621
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.069	0.05	3809
X-RAY DIFFRACTION	r_ncsr_local_group_16	0.078	0.05	3840
X-RAY DIFFRACTION	r_ncsr_local_group_17	0.065	0.05	3656
X-RAY DIFFRACTION	r_ncsr_local_group_18	0.072	0.05	3853
X-RAY DIFFRACTION	r_ncsr_local_group_19	0.067	0.05	3817
X-RAY DIFFRACTION	r_ncsr_local_group_20	0.06	0.05	4079
X-RAY DIFFRACTION	r_ncsr_local_group_21	0.066	0.05	3806

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 (%)
2.6-2.668	0.435	149	0.413	2914	X-RAY DIFFRACTION	100
2.668-2.741	0.387	126	0.404	2833	X-RAY DIFFRACTION	100
2.741-2.82	0.428	145	0.397	2765	X-RAY DIFFRACTION	99.9313
2.82-2.907	0.414	142	0.375	2656	X-RAY DIFFRACTION	99.8929
2.907-3.002	0.402	138	0.376	2581	X-RAY DIFFRACTION	99.7432
3.002-3.107	0.371	133	0.378	2525	X-RAY DIFFRACTION	99.9248
3.107-3.224	0.368	124	0.376	2429	X-RAY DIFFRACTION	99.6876
3.224-3.356	0.39	116	0.345	2318	X-RAY DIFFRACTION	99.8769
3.356-3.505	0.376	120	0.319	2245	X-RAY DIFFRACTION	99.7049
3.505-3.675	0.296	127	0.295	2146	X-RAY DIFFRACTION	99.9121
3.675-3.874	0.296	122	0.296	2027	X-RAY DIFFRACTION	99.7679
3.874-4.108	0.307	115	0.266	1901	X-RAY DIFFRACTION	99.115
4.108-4.391	0.245	79	0.224	1850	X-RAY DIFFRACTION	99.6899
4.391-4.742	0.189	101	0.186	1702	X-RAY DIFFRACTION	99.8892
4.742-5.193	0.199	83	0.204	1561	X-RAY DIFFRACTION	100
5.193-5.803	0.244	54	0.24	1464	X-RAY DIFFRACTION	99.9342
5.803-6.695	0.276	65	0.268	1290	X-RAY DIFFRACTION	100
6.695-8.187	0.263	65	0.245	1086	X-RAY DIFFRACTION	100
8.187-11.525	0.267	54	0.236	848	X-RAY DIFFRACTION	100
11.525-14.5	0.306	34	0.385	512	X-RAY DIFFRACTION	99.0926

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	1.8013	-1.9362	0.866	4.3894	0.3598	3.0971	-0.0035	0.1165	0.2008	-0.1685	-0.1614	-0.4289	-1.0051	0.9921	0.1649	0.869	-0.3968	-0.0674	0.5541	0.0939	0.0626	-27.6296	-13.7312	-58.4183
2	3.4177	0.3645	1.5614	2.6024	0.7441	4.803	-0.2794	0.3122	0.0696	0.0434	0.2172	0.1722	-0.093	0.8686	0.0622	0.359	0.0818	-0.002	0.4517	0.0005	0.013	-28.3221	-40.2481	-63.2459
3	1.9525	-0.0471	-0.7998	2.8149	-0.1008	7.8165	-0.0289	0.191	-0.0898	0.0922	-0.0295	0.1279	-0.1089	0.9026	0.0584	0.3072	-0.0436	-0.0223	0.5829	0.0799	0.0286	-30.339	-38.3455	-2.6832
4	1.838	0.0268	0.4748	7.6783	-4.2433	6.7229	-0.0403	-0.7336	-0.0639	1.657	-0.5423	-0.1442	-2.7081	1.2548	0.5826	1.6526	-0.5147	-0.1963	0.7487	0.1532	0.0797	-31.0541	-13.0348	-10.1032
5	1.2506	-1.1048	0.0229	2.5064	-0.4239	3.0056	0.0304	-0.1625	-0.0321	0.3477	-0.2252	-0.1225	-1.0263	0.6655	0.1948	1.7482	-0.6699	-0.1947	0.4257	0.0948	0.0331	-29.0757	-1.8302	-34.4391
6	3.8972	1.8518	-0.4817	4.7281	2.3929	6.4738	0.0639	-0.1771	-0.3197	0.4351	-0.0522	0.0243	1.9631	1.1112	-0.0117	1.1683	0.4685	-0.028	0.6073	0.0665	0.0635	-29.8348	-59.9757	-19.2854
7	2.224	1.285	0.3925	2.9355	0.3406	3.9538	-0.0843	-0.0366	-0.1179	0.2377	0.0895	0.0755	1.054	0.4993	-0.0052	1.1052	0.4381	-0.0032	0.3752	0.0041	0.0168	-28.792	-60.4372	-45.5736

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	B	6 - 144
2	X-RAY DIFFRACTION	2	G	5 - 144
3	X-RAY DIFFRACTION	3	A	5 - 201
4	X-RAY DIFFRACTION	4	D	5 - 144
5	X-RAY DIFFRACTION	5	E	5 - 144
6	X-RAY DIFFRACTION	6	F	10 - 144
7	X-RAY DIFFRACTION	7	C	5 - 144

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