PDB-7w62: Mevo lectin complex with mannotetraose (Man4)

ID or keywords:

Entry

Database: PDB / ID: 7w62

Title

Mevo lectin complex with mannotetraose (Man4)

Components

lectin

Keywords

SUGAR BINDING PROTEIN / Mevo lectin /

mannose-binding lectin / heptamer

Function / homology

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

Function and homology information

Biological species

Methanococcus voltae A3 (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Sivaji, N. / Vijayan, M.

Funding support

India, 1items

Citation

Journal: To Be Published
Title: Mevo lectin complex with mannotetraose (Man4)
Authors: Sivaji, N. / Vijayan, M.

History

Deposition	Dec 1, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 18, 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

-
Download

PDBx/mmCIF format	7w62.cif.gz	397.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7w62.ent.gz	326.2 KB	Display	PDB format
PDBx/mmJSON format	7w62.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w6/7w62 ftp://data.pdbj.org/pub/pdb/validation_reports/w6/7w62	HTTPS FTP

-
Related structure data

Related structure data	7dedS S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
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

230 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
115 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
115 kDa, 7 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	96.210, 168.300, 170.249
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein

lectin /

Mass: 15783.812 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Methanococcus voltae 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-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose

Type: oligosaccharide

/ Mass: 666.578 Da / Num. of mol.: 12 / Source method: obtained synthetically

Descriptor	Type	Program
DManpa1-2DManpa1-2DManpa1-2DManpa1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,4,3/[a1122h-1a_1-5]/1-1-1-1/a2-b1_b2-c1_c2-d1	WURCS	PDB2Glycan 1.1.0
[][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}	LINUCS	PDB-CARE

#3: Polysaccharide

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

Type: oligosaccharide

/ Mass: 504.438 Da / Num. of mol.: 2 / Source method: obtained synthetically

Descriptor	Type	Program
DManpa1-2DManpa1-2DManpa1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,3,2/[a1122h-1a_1-5]/1-1-1/a2-b1_b2-c1	WURCS	PDB2Glycan 1.1.0
[][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}	LINUCS	PDB-CARE

#4: Chemical

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

Ethylene glycol

Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₆O₂

#5: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 525 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.9 Å³/Da / Density % sol: 57.75 %
Crystal grow	Temperature: 295 K / Method: microbatch / pH: 6 Details: Tacsimate pH 6.0, 0.1 M MES monohydrate pH 6.0, 25% (w/v) polyethylene glycol 4000

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 5, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2→96.21 Å / Num. obs: 2231847 / % possible obs: 100 % / Redundancy: 12 % / CC_1/2: 0.99 / R_merge(I) obs: 0.14 / Net I/σ(I): 12.1
Reflection shell	Resolution: 2→2.11 Å / R_merge(I) obs: 1.33 / Num. unique obs: 186472 / CC_1/2: 0.68

-
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: 7DED

7ded

Resolution: 2→85.27 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.937 / 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	0.2496	9317	5.002 %
R_work	0.2259	176948	-
all	0.227	-	-
obs	-	186265	99.946 %

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: 34.575 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.349 Å²	0 Å²	0 Å²
2-	-	-1.499 Å²	0 Å²
3-	-	-	-1.851 Å²

Refinement step

Cycle: LAST / Resolution: 2→85.27 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14899	0	636	525	16060

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.014	15833
X-RAY DIFFRACTION	r_bond_other_d	0.036	0.018	14466
X-RAY DIFFRACTION	r_angle_refined_deg	1.619	1.7	21417
X-RAY DIFFRACTION	r_angle_other_deg	2.365	1.649	33821
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.062	5	1948
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.641	24.565	644
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.931	15	2623
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	10.217	15	28
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	2358
X-RAY DIFFRACTION	r_chiral_restr_other	0.016	0.2	54
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	16996
X-RAY DIFFRACTION	r_gen_planes_other	0.012	0.02	3040
X-RAY DIFFRACTION	r_nbd_refined	0.173	0.2	2239
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.213	0.2	13531
X-RAY DIFFRACTION	r_nbtor_refined	0.162	0.2	7866
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	6665
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.154	0.2	597
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.043	0.2	5
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.272	0.2	35
X-RAY DIFFRACTION	r_nbd_other	0.284	0.2	139
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.183	0.2	20
X-RAY DIFFRACTION	r_mcbond_it	3.092	3.46	7834
X-RAY DIFFRACTION	r_mcbond_other	3.088	3.46	7833
X-RAY DIFFRACTION	r_mcangle_it	4.357	5.177	9768
X-RAY DIFFRACTION	r_mcangle_other	4.358	5.177	9769
X-RAY DIFFRACTION	r_scbond_it	4.047	3.998	7999
X-RAY DIFFRACTION	r_scbond_other	4.047	3.998	8000
X-RAY DIFFRACTION	r_scangle_it	5.86	5.851	11649
X-RAY DIFFRACTION	r_scangle_other	5.86	5.851	11650
X-RAY DIFFRACTION	r_lrange_it	7.442	42.083	16404
X-RAY DIFFRACTION	r_lrange_other	7.433	42.03	16351
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.048	0.05	4325
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.031	0.05	4350
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.041	0.05	4339
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.049	0.05	4285
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.023	0.05	4367
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.048	0.05	4304
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.018	0.05	4380
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.042	0.05	4327
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.023	0.05	4366
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.041	0.05	4365
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.032	0.05	4337
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.023	0.05	4370
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.041	0.05	4312
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.048	0.05	4320
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.058	0.05	4263
X-RAY DIFFRACTION	r_ncsr_local_group_16	0.061	0.05	4248
X-RAY DIFFRACTION	r_ncsr_local_group_17	0.041	0.05	4321
X-RAY DIFFRACTION	r_ncsr_local_group_18	0.056	0.05	4268
X-RAY DIFFRACTION	r_ncsr_local_group_19	0.047	0.05	4315
X-RAY DIFFRACTION	r_ncsr_local_group_20	0.055	0.05	4314
X-RAY DIFFRACTION	r_ncsr_local_group_21	0.044	0.05	4333
X-RAY DIFFRACTION	r_ncsr_local_group_22	0.057	0.05	4310
X-RAY DIFFRACTION	r_ncsr_local_group_23	0.054	0.05	4288
X-RAY DIFFRACTION	r_ncsr_local_group_24	0.044	0.05	4325
X-RAY DIFFRACTION	r_ncsr_local_group_25	0.055	0.05	4277
X-RAY DIFFRACTION	r_ncsr_local_group_26	0.04	0.05	4290
X-RAY DIFFRACTION	r_ncsr_local_group_27	0.051	0.05	4258
X-RAY DIFFRACTION	r_ncsr_local_group_28	0.022	0.05	4336
X-RAY DIFFRACTION	r_ncsr_local_group_29	0.048	0.05	4289
X-RAY DIFFRACTION	r_ncsr_local_group_30	0.027	0.05	4342
X-RAY DIFFRACTION	r_ncsr_local_group_31	0.028	0.05	4347
X-RAY DIFFRACTION	r_ncsr_local_group_32	0.029	0.05	4354
X-RAY DIFFRACTION	r_ncsr_local_group_33	0.044	0.05	4321
X-RAY DIFFRACTION	r_ncsr_local_group_34	0.04	0.05	4315
X-RAY DIFFRACTION	r_ncsr_local_group_35	0.023	0.05	4338
X-RAY DIFFRACTION	r_ncsr_local_group_36	0.04	0.05	4300
X-RAY DIFFRACTION	r_ncsr_local_group_37	0.049	0.05	4257
X-RAY DIFFRACTION	r_ncsr_local_group_38	0.04	0.05	4300
X-RAY DIFFRACTION	r_ncsr_local_group_39	0.056	0.05	4247
X-RAY DIFFRACTION	r_ncsr_local_group_40	0.041	0.05	4307
X-RAY DIFFRACTION	r_ncsr_local_group_41	0.047	0.05	4275
X-RAY DIFFRACTION	r_ncsr_local_group_42	0.043	0.05	4300
X-RAY DIFFRACTION	r_ncsr_local_group_43	0.037	0.05	4345
X-RAY DIFFRACTION	r_ncsr_local_group_44	0.046	0.05	4273
X-RAY DIFFRACTION	r_ncsr_local_group_45	0.04	0.05	4314
X-RAY DIFFRACTION	r_ncsr_local_group_46	0.052	0.05	4258
X-RAY DIFFRACTION	r_ncsr_local_group_47	0.048	0.05	4290
X-RAY DIFFRACTION	r_ncsr_local_group_48	0.051	0.05	4350
X-RAY DIFFRACTION	r_ncsr_local_group_49	0.047	0.05	4283
X-RAY DIFFRACTION	r_ncsr_local_group_50	0.054	0.05	4258
X-RAY DIFFRACTION	r_ncsr_local_group_51	0.049	0.05	4274
X-RAY DIFFRACTION	r_ncsr_local_group_52	0.057	0.05	4260
X-RAY DIFFRACTION	r_ncsr_local_group_53	0.038	0.05	4313
X-RAY DIFFRACTION	r_ncsr_local_group_54	0.048	0.05	4289
X-RAY DIFFRACTION	r_ncsr_local_group_55	0.055	0.05	4256
X-RAY DIFFRACTION	r_ncsr_local_group_56	0.042	0.05	4311
X-RAY DIFFRACTION	r_ncsr_local_group_57	0.018	0.05	4356
X-RAY DIFFRACTION	r_ncsr_local_group_58	0.035	0.05	4321
X-RAY DIFFRACTION	r_ncsr_local_group_59	0.022	0.05	4346
X-RAY DIFFRACTION	r_ncsr_local_group_60	0.037	0.05	4335
X-RAY DIFFRACTION	r_ncsr_local_group_61	0.031	0.05	4329
X-RAY DIFFRACTION	r_ncsr_local_group_62	0.008	0.05	4368
X-RAY DIFFRACTION	r_ncsr_local_group_63	0.034	0.05	4306
X-RAY DIFFRACTION	r_ncsr_local_group_64	0.046	0.05	4296
X-RAY DIFFRACTION	r_ncsr_local_group_65	0.054	0.05	4261
X-RAY DIFFRACTION	r_ncsr_local_group_66	0.048	0.05	4302
X-RAY DIFFRACTION	r_ncsr_local_group_67	0.057	0.05	4278
X-RAY DIFFRACTION	r_ncsr_local_group_68	0.047	0.05	4309
X-RAY DIFFRACTION	r_ncsr_local_group_69	0.042	0.05	4307
X-RAY DIFFRACTION	r_ncsr_local_group_70	0.048	0.05	4279
X-RAY DIFFRACTION	r_ncsr_local_group_71	0.039	0.05	4322
X-RAY DIFFRACTION	r_ncsr_local_group_72	0.018	0.05	4366
X-RAY DIFFRACTION	r_ncsr_local_group_73	0.035	0.05	4342
X-RAY DIFFRACTION	r_ncsr_local_group_74	0.029	0.05	4329
X-RAY DIFFRACTION	r_ncsr_local_group_75	0.018	0.05	4363
X-RAY DIFFRACTION	r_ncsr_local_group_76	0.039	0.05	4304
X-RAY DIFFRACTION	r_ncsr_local_group_77	0.04	0.05	4334
X-RAY DIFFRACTION	r_ncsr_local_group_78	0.051	0.05	4308
X-RAY DIFFRACTION	r_ncsr_local_group_79	0.047	0.05	4297
X-RAY DIFFRACTION	r_ncsr_local_group_80	0.036	0.05	4324
X-RAY DIFFRACTION	r_ncsr_local_group_81	0.049	0.05	4280
X-RAY DIFFRACTION	r_ncsr_local_group_82	0.038	0.05	4332
X-RAY DIFFRACTION	r_ncsr_local_group_83	0.033	0.05	4328
X-RAY DIFFRACTION	r_ncsr_local_group_84	0.022	0.05	4355
X-RAY DIFFRACTION	r_ncsr_local_group_85	0.041	0.05	4304
X-RAY DIFFRACTION	r_ncsr_local_group_86	0.044	0.05	4312
X-RAY DIFFRACTION	r_ncsr_local_group_87	0.038	0.05	4340
X-RAY DIFFRACTION	r_ncsr_local_group_88	0.051	0.05	4294
X-RAY DIFFRACTION	r_ncsr_local_group_89	0.03	0.05	4344
X-RAY DIFFRACTION	r_ncsr_local_group_90	0.044	0.05	4314
X-RAY DIFFRACTION	r_ncsr_local_group_91	0.034	0.05	4317

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 (%)
2-2.052	0.332	678	0.328	12963	X-RAY DIFFRACTION	99.956
2.052-2.108	0.365	702	0.339	12596	X-RAY DIFFRACTION	99.9324
2.108-2.169	0.333	633	0.336	12292	X-RAY DIFFRACTION	99.9227
2.169-2.236	0.329	618	0.306	11968	X-RAY DIFFRACTION	99.9047
2.236-2.309	0.324	641	0.292	11557	X-RAY DIFFRACTION	99.8772
2.309-2.39	0.284	617	0.261	11198	X-RAY DIFFRACTION	99.9408
2.39-2.481	0.27	544	0.244	10888	X-RAY DIFFRACTION	99.9563
2.481-2.582	0.276	537	0.243	10444	X-RAY DIFFRACTION	99.9909
2.582-2.696	0.266	573	0.236	9960	X-RAY DIFFRACTION	99.9715
2.696-2.828	0.254	548	0.227	9545	X-RAY DIFFRACTION	99.9604
2.828-2.981	0.246	484	0.209	9138	X-RAY DIFFRACTION	99.9896
2.981-3.162	0.236	426	0.211	8700	X-RAY DIFFRACTION	99.989
3.162-3.38	0.233	436	0.222	8141	X-RAY DIFFRACTION	99.9883
3.38-3.65	0.241	425	0.222	7582	X-RAY DIFFRACTION	99.9875
3.65-3.998	0.225	353	0.203	7045	X-RAY DIFFRACTION	99.946
3.998-4.47	0.161	286	0.159	6417	X-RAY DIFFRACTION	100
4.47-5.16	0.185	259	0.157	5706	X-RAY DIFFRACTION	99.9832
5.16-6.317	0.239	237	0.207	4839	X-RAY DIFFRACTION	100
6.317-8.921	0.223	216	0.21	3769	X-RAY DIFFRACTION	99.8997
8.921-85.1	0.269	104	0.245	2200	X-RAY DIFFRACTION	99.3103

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi