PDB-6t99: Crystal structrue of RSL W31YW76Y lectin mutant in complex with a...

ID or keywords:

Entry

Database: PDB / ID: 6t99

Title

Crystal structrue of RSL W31YW76Y lectin mutant in complex with alpha-methylfucoside

Components

Fucose-binding lectin protein

Keywords

SUGAR BINDING PROTEIN / lectin / beta-propeller / fucose-binding

Function / homology

Function and homology information

carbohydrate binding / metal ion binding
Similarity search - Function

Biological species

Ralstonia solanacearum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Houser, J. / Kozmon, S. / Wimmerova, M.

Citation

Journal: Chemistry / Year: 2020
Title: The CH-pi Interaction in Protein-Carbohydrate Binding: Bioinformatics and In Vitro Quantification.
Authors: Houser, J. / Kozmon, S. / Mishra, D. / Hammerova, Z. / Wimmerova, M. / Koca, J.

History

Deposition	Oct 26, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 22, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2	Aug 12, 2020	Group: Database references / Structure summary / Category: chem_comp / citation / citation_author Item: _chem_comp.pdbx_synonyms / _citation.title / _citation_author.identifier_ORCID
Revision 1.3	Dec 16, 2020	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4	Jan 24, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6t99.cif.gz	166.4 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6t99_validation.pdf.gz	5.2 MB	Display	wwPDB validaton report
Full document	6t99_full_validation.pdf.gz	5.2 MB	Display
Data in XML	6t99_validation.xml.gz	27 KB	Display
Data in CIF	6t99_validation.cif.gz	40 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t9/6t99 ftp://data.pdbj.org/pub/pdb/validation_reports/t9/6t99	HTTPS FTP

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Related structure data

Related structure data	6t9aC 6t9bC 2bt9S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6f7y-2 4csd-1 6t9b-3 6stz-2 2bs6-d 6stz-1 3zw0-d 4csd-2 6t9b-1 7k2c-1 Search similar-shape structures by Omokage search (details) 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 - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

6t9aC

6t9bC

2bt9S

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Fucose-binding lectin protein

B: Fucose-binding lectin protein

C: Fucose-binding lectin protein

D: Fucose-binding lectin protein

E: Fucose-binding lectin protein

F: Fucose-binding lectin protein

G: Fucose-binding lectin protein

H: Fucose-binding lectin protein

I: Fucose-binding lectin protein

hetero molecules

90.4 kDa, 9 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Fucose-binding lectin protein

B: Fucose-binding lectin protein

C: Fucose-binding lectin protein

hetero molecules

defined by author
30.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Fucose-binding lectin protein

E: Fucose-binding lectin protein

F: Fucose-binding lectin protein

hetero molecules

defined by author
30.2 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

G: Fucose-binding lectin protein

H: Fucose-binding lectin protein

I: Fucose-binding lectin protein

hetero molecules

defined by author
30.2 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	36.602, 44.425, 116.574
Angle α, β, γ (deg.)	96.420, 98.700, 103.360
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: THR / End label comp-ID: THR / Refine code: _

Dom-ID	Ens-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	A	A	3 - 88	2 - 87
2	1	B	B	3 - 88	2 - 87
1	2	A	A	3 - 90	2 - 89
2	2	C	C	3 - 90	2 - 89
1	3	A	A	3 - 90	2 - 89
2	3	D	D	3 - 90	2 - 89
1	4	A	A	3 - 90	2 - 89
2	4	E	E	3 - 90	2 - 89
1	5	A	A	3 - 90	2 - 89
2	5	F	F	3 - 90	2 - 89
1	6	A	A	3 - 90	2 - 89
2	6	G	G	3 - 90	2 - 89
1	7	A	A	3 - 90	2 - 89
2	7	H	H	3 - 90	2 - 89
1	8	A	A	3 - 90	2 - 89
2	8	I	I	3 - 90	2 - 89
1	9	B	B	3 - 88	2 - 87
2	9	C	C	3 - 88	2 - 87
1	10	B	B	3 - 88	2 - 87
2	10	D	D	3 - 88	2 - 87
1	11	B	B	3 - 88	2 - 87
2	11	E	E	3 - 88	2 - 87
1	12	B	B	3 - 88	2 - 87
2	12	F	F	3 - 88	2 - 87
1	13	B	B	3 - 88	2 - 87
2	13	G	G	3 - 88	2 - 87
1	14	B	B	3 - 88	2 - 87
2	14	H	H	3 - 88	2 - 87
1	15	B	B	3 - 88	2 - 87
2	15	I	I	3 - 88	2 - 87
1	16	C	C	3 - 90	2 - 89
2	16	D	D	3 - 90	2 - 89
1	17	C	C	3 - 90	2 - 89
2	17	E	E	3 - 90	2 - 89
1	18	C	C	3 - 90	2 - 89
2	18	F	F	3 - 90	2 - 89
1	19	C	C	3 - 90	2 - 89
2	19	G	G	3 - 90	2 - 89
1	20	C	C	3 - 90	2 - 89
2	20	H	H	3 - 90	2 - 89
1	21	C	C	3 - 90	2 - 89
2	21	I	I	3 - 90	2 - 89
1	22	D	D	3 - 90	2 - 89
2	22	E	E	3 - 90	2 - 89
1	23	D	D	3 - 90	2 - 89
2	23	F	F	3 - 90	2 - 89
1	24	D	D	3 - 90	2 - 89
2	24	G	G	3 - 90	2 - 89
1	25	D	D	3 - 90	2 - 89
2	25	H	H	3 - 90	2 - 89
1	26	D	D	3 - 90	2 - 89
2	26	I	I	3 - 90	2 - 89
1	27	E	E	3 - 90	2 - 89
2	27	F	F	3 - 90	2 - 89
1	28	E	E	3 - 90	2 - 89
2	28	G	G	3 - 90	2 - 89
1	29	E	E	3 - 90	2 - 89
2	29	H	H	3 - 90	2 - 89
1	30	E	E	3 - 90	2 - 89
2	30	I	I	3 - 90	2 - 89
1	31	F	F	3 - 90	2 - 89
2	31	G	G	3 - 90	2 - 89
1	32	F	F	3 - 90	2 - 89
2	32	H	H	3 - 90	2 - 89
1	33	F	F	3 - 90	2 - 89
2	33	I	I	3 - 90	2 - 89
1	34	G	G	3 - 90	2 - 89
2	34	H	H	3 - 90	2 - 89
1	35	G	G	3 - 90	2 - 89
2	35	I	I	3 - 90	2 - 89
1	36	H	H	3 - 90	2 - 89
2	36	I	I	3 - 90	2 - 89

NCS ensembles :

#1: Protein

Fucose-binding lectin protein / Putative fucose-binding lectin protein

Mass: 9687.491 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Details: Double mutant W31Y W76Y / Source: (gene. exp.)

Ralstonia solanacearum (bacteria)
Gene: RSP795_21825, RSP799_05830, RSP822_19650, RUN39_v1_50103
Production host:

Escherichia coli (E. coli) / References: UniProt: A0A0S4TLR1

#2: Sugar

ChemComp-MFU / methyl alpha-L-fucopyranoside / ALPHA-L-METHYL-FUCOSE / methyl 6-deoxy-alpha-L-galactopyranoside / methyl alpha-L-fucoside / methyl L-fucoside / methyl fucoside

Type: L-saccharide / Mass: 178.183 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Formula: C₇H₁₄O₅ / Feature type: SUBJECT OF INVESTIGATION

#3: Chemical

ChemComp-NA / SODIUM ION

Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 114 / 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 Å³/Da / Density % sol: 38.6 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2 / Details: 26% PEG6K, 0.1M Tris/HCl, pH 8.2

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 12, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 2.7→42.72 Å / Num. obs: 18743 / % possible obs: 97.6 % / Redundancy: 1.8 % / CC_1/2: 0.971 / R_merge(I) obs: 0.127 / Net I/σ(I): 4.1 / Num. measured all: 34335
Reflection shell	Resolution: 2.7→2.83 Å / Redundancy: 1.9 % / R_merge(I) obs: 0.464 / Num. unique obs: 2528 / CC_1/2: 0.649 / % possible all: 96.9

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Processing

Software

Name	Version	Classification
Aimless	0.5.32	data scaling
REFMAC	5.8.0238	refinement
PDB_EXTRACT	3.25	data extraction
XDS		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2BT9

2bt9

Resolution: 2.7→42.72 Å / Cor.coef. F_o:F_c: 0.917 / Cor.coef. F_o:F_c free: 0.877 / SU B: 21.227 / SU ML: 0.398 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.437
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2648	898	4.8 %	RANDOM
R_work	0.2198	-	-	-
obs	0.2219	17830	97.52 %	-

Solvent computation

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

Displacement parameters

B_iso max: 85.63 Å² / B_iso mean: 35.682 Å² / B_iso min: 10 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.98 Å²	3.14 Å²	-0.75 Å²
2-	-	0.66 Å²	0.59 Å²
3-	-	-	-3.76 Å²

Refinement step

Cycle: final / Resolution: 2.7→42.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6008	0	218	114	6340
B_iso mean	-	-	32.63	26.52	-
Num. residues	-	-	-	-	791

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.013	6395
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.018	5410
X-RAY DIFFRACTION	r_angle_refined_deg	1.367	1.698	8784
X-RAY DIFFRACTION	r_angle_other_deg	1.207	1.629	12515
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.155	5	782
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.676	21.877	277
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.823	15	816
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.81	15	27
X-RAY DIFFRACTION	r_chiral_restr	0.047	0.2	952
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	7077
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1448

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	2484	0.08
1	2	B	2484	0.08
2	1	A	2479	0.1
2	2	C	2479	0.1
3	1	A	2506	0.08
3	2	D	2506	0.08
4	1	A	2482	0.1
4	2	E	2482	0.1
5	1	A	2497	0.09
5	2	F	2497	0.09
6	1	A	2481	0.09
6	2	G	2481	0.09
7	1	A	2501	0.1
7	2	H	2501	0.1
8	1	A	2500	0.1
8	2	I	2500	0.1
9	1	B	2484	0.08
9	2	C	2484	0.08
10	1	B	2504	0.07
10	2	D	2504	0.07
11	1	B	2507	0.07
11	2	E	2507	0.07
12	1	B	2476	0.07
12	2	F	2476	0.07
13	1	B	2492	0.08
13	2	G	2492	0.08
14	1	B	2507	0.08
14	2	H	2507	0.08
15	1	B	2508	0.08
15	2	I	2508	0.08
16	1	C	2529	0.09
16	2	D	2529	0.09
17	1	C	2518	0.1
17	2	E	2518	0.1
18	1	C	2520	0.1
18	2	F	2520	0.1
19	1	C	2507	0.09
19	2	G	2507	0.09
20	1	C	2527	0.1
20	2	H	2527	0.1
21	1	C	2473	0.11
21	2	I	2473	0.11
22	1	D	2497	0.08
22	2	E	2497	0.08
23	1	D	2549	0.07
23	2	F	2549	0.07
24	1	D	2528	0.09
24	2	G	2528	0.09
25	1	D	2522	0.1
25	2	H	2522	0.1
26	1	D	2469	0.1
26	2	I	2469	0.1
27	1	E	2512	0.08
27	2	F	2512	0.08
28	1	E	2492	0.1
28	2	G	2492	0.1
29	1	E	2545	0.1
29	2	H	2545	0.1
30	1	E	2495	0.1
30	2	I	2495	0.1
31	1	F	2551	0.09
31	2	G	2551	0.09
32	1	F	2500	0.1
32	2	H	2500	0.1
33	1	F	2471	0.1
33	2	I	2471	0.1
34	1	G	2496	0.1
34	2	H	2496	0.1
35	1	G	2477	0.11
35	2	I	2477	0.11
36	1	H	2490	0.11
36	2	I	2490	0.11

LS refinement shell

Resolution: 2.7→2.77 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.337	74	-
R_work	0.333	1345	-
all	-	1419	-
obs	-	-	96.93 %

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