PDB-7btl: Mevo lectin complex with mannopentose

ID or keywords:

Entry

Database: PDB / ID: 7btl

Title

Mevo lectin complex with mannopentose

Components

lectin

Keywords

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

Function / homology

Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain superfamily / 6alpha-alpha-mannobiose / alpha-D-mannopyranose / Jacalin-type lectin domain-containing protein

Function and homology information

Biological species

Methanococcus voltae (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.25 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	7btl.cif.gz	204.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7btl.ent.gz	163.2 KB	Display	PDB format
PDBx/mmJSON format	7btl.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7btl_validation.pdf.gz	2.9 MB	Display	wwPDB validaton report
Full document	7btl_full_validation.pdf.gz	3 MB	Display
Data in XML	7btl_validation.xml.gz	41 KB	Display
Data in CIF	7btl_validation.cif.gz	55.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bt/7btl ftp://data.pdbj.org/pub/pdb/validation_reports/bt/7btl	HTTPS FTP

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Related structure data

Related structure data	7bsbC 7bsmC 7bsnC 7bt8SC 7bt9C 7bthC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7bt8-d 7bsm-1 7bsn-2 7bsn-1 7bsb-1 7bt9-2 7bt9-1 7ded-d 7bsb-2 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
Related items in Molecule of the Month	#247 - Jul 2020 Myelin-associated Glycoprotein similarity (1) #74 - Feb 2006 alpha-Amylase similarity (1) #83 - Nov 2006 Fibrin similarity (1)

Deposited unit

B: lectin

G: lectin

A: lectin

D: lectin

E: lectin

F: lectin

C: lectin

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	51.830, 168.940, 169.780
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P22₁2₁

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Protein , 1 types, 7 molecules BGADEFC

#1: Protein	lectin Mass: 15210.124 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

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Sugars , 4 types, 8 molecules

#2: Polysaccharide

alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose

Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DManpa1-6DManpa1-6[DManpa1-3]DManpa1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,4,3/[a1122h-1a_1-5]/1-1-1-1/a3-b1_a6-c1_c6-d1	WURCS	PDB2Glycan 1.1.0
[][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}	LINUCS	PDB-CARE

#3: Polysaccharide

alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose

Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DManpa1-3[DManpa1-6]DManpa1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,3,2/[a1122h-1a_1-5]/1-1-1/a3-b1_a6-c1	WURCS	PDB2Glycan 1.1.0
[][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}	LINUCS	PDB-CARE

#4: Polysaccharide

alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose / 6alpha-alpha-mannobiose

Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 6alpha-alpha-mannobiose

#5: Sugar

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

Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C₆H₁₂O₆ / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 2 types, 164 molecules

#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C₃H₈O₃
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 3.49 Å³/Da / Density % sol: 59.48 %
Crystal grow	Temperature: 296 K / Method: microbatch / pH: 6 Details: 6%(v/v) Tacsimate pH 6.0, 0.1 M MES monohydrate pH 6.0, 25%(w/v) polyethylene glycol 4000

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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: 0.999 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 11, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.999 Å / Relative weight: 1
Reflection	Resolution: 2.25→85.04 Å / Num. obs: 71908 / % possible obs: 100 % / Redundancy: 6.7 % / CC_1/2: 0.98 / R_merge(I) obs: 0.21 / Net I/σ(I): 5.8
Reflection shell	Resolution: 2.25→2.37 Å / Redundancy: 6.7 % / R_merge(I) obs: 0.47 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 10315 / CC_1/2: 0.75 / % 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: 7BT8

7bt8

Resolution: 2.25→85.034 Å / Cor.coef. F_o:F_c: 0.909 / Cor.coef. F_o:F_c free: 0.879 / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.228
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2949	3567	4.966 %
R_work	0.2527	68258	-
all	0.255	-	-
obs	-	71825	99.964 %

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: 32.851 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.726 Å²	0 Å²	-0 Å²
2-	-	-1.886 Å²	0 Å²
3-	-	-	-1.84 Å²

Refinement step

Cycle: LAST / Resolution: 2.25→85.034 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7396	0	244	163	7803

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.013	7784
X-RAY DIFFRACTION	r_bond_other_d	0.036	0.018	7107
X-RAY DIFFRACTION	r_angle_refined_deg	2.124	1.686	10531
X-RAY DIFFRACTION	r_angle_other_deg	2.515	1.636	16578
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.721	5	971
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.595	24.713	314
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.821	15	1286
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	8.301	15	12
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	1148
X-RAY DIFFRACTION	r_chiral_restr_other	0.569	0.2	21
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	8445
X-RAY DIFFRACTION	r_gen_planes_other	0.018	0.02	1503
X-RAY DIFFRACTION	r_nbd_refined	0.186	0.2	1229
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.226	0.2	6667
X-RAY DIFFRACTION	r_nbtor_refined	0.171	0.2	3745
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	3574
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.194	0.2	168
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.164	0.2	7
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.254	0.2	25
X-RAY DIFFRACTION	r_nbd_other	0.254	0.2	72
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.44	0.2	13
X-RAY DIFFRACTION	r_mcbond_it	5.052	3.412	3908
X-RAY DIFFRACTION	r_mcbond_other	5.05	3.412	3907
X-RAY DIFFRACTION	r_mcangle_it	7.356	5.101	4871
X-RAY DIFFRACTION	r_mcangle_other	7.355	5.102	4872
X-RAY DIFFRACTION	r_scbond_it	5.3	3.835	3876
X-RAY DIFFRACTION	r_scbond_other	5.3	3.835	3877
X-RAY DIFFRACTION	r_scangle_it	7.53	5.621	5660
X-RAY DIFFRACTION	r_scangle_other	7.529	5.621	5661
X-RAY DIFFRACTION	r_lrange_it	10.553	66.051	31437
X-RAY DIFFRACTION	r_lrange_other	10.553	66.055	31405
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.104	0.05	3908
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.072	0.05	4198
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.087	0.05	4132
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.085	0.05	4133
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.07	0.05	4208
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.085	0.05	4118
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.112	0.05	3864
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.108	0.05	3915
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.099	0.05	3935
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.101	0.05	3940
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.094	0.05	3928
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.097	0.05	4075
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.09	0.05	4102
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.079	0.05	4137
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.091	0.05	4073
X-RAY DIFFRACTION	r_ncsr_local_group_16	0.095	0.05	4100
X-RAY DIFFRACTION	r_ncsr_local_group_17	0.082	0.05	4150
X-RAY DIFFRACTION	r_ncsr_local_group_18	0.081	0.05	4135
X-RAY DIFFRACTION	r_ncsr_local_group_19	0.071	0.05	4170
X-RAY DIFFRACTION	r_ncsr_local_group_20	0.081	0.05	4101
X-RAY DIFFRACTION	r_ncsr_local_group_21	0.075	0.05	4130

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 (%)
2.25-2.308	0.343	251	0.333	4936	X-RAY DIFFRACTION	99.9422
2.308-2.372	0.394	263	0.328	4852	X-RAY DIFFRACTION	99.9414
2.372-2.44	0.347	231	0.312	4732	X-RAY DIFFRACTION	99.9597
2.44-2.515	0.362	241	0.312	4564	X-RAY DIFFRACTION	99.9376
2.515-2.598	0.318	248	0.288	4493	X-RAY DIFFRACTION	99.9578
2.598-2.689	0.336	208	0.297	4309	X-RAY DIFFRACTION	99.9336
2.689-2.791	0.374	240	0.291	4110	X-RAY DIFFRACTION	99.9081
2.791-2.904	0.347	207	0.275	4051	X-RAY DIFFRACTION	99.9765
2.904-3.033	0.353	196	0.272	3878	X-RAY DIFFRACTION	99.9755
3.033-3.181	0.308	182	0.257	3692	X-RAY DIFFRACTION	100
3.181-3.353	0.314	201	0.267	3502	X-RAY DIFFRACTION	100
3.353-3.557	0.288	173	0.264	3330	X-RAY DIFFRACTION	99.9715
3.557-3.802	0.313	154	0.267	3167	X-RAY DIFFRACTION	100
3.802-4.106	0.275	139	0.228	2966	X-RAY DIFFRACTION	100
4.106-4.498	0.213	155	0.19	2711	X-RAY DIFFRACTION	100
4.498-5.028	0.209	149	0.178	2461	X-RAY DIFFRACTION	100
5.028-5.804	0.276	124	0.206	2212	X-RAY DIFFRACTION	100
5.804-7.104	0.231	90	0.192	1890	X-RAY DIFFRACTION	100
7.104-10.029	0.162	80	0.189	1497	X-RAY DIFFRACTION	99.9366
10.029-14.754	0.383	35	0.265	905	X-RAY DIFFRACTION	99.8937

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Protein , 1 types, 7 molecules BGADEFC

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Sugars , 4 types, 8 molecules

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Non-polymers , 2 types, 164 molecules

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