PDB-8cf6: Dimethylated RSL-R5 in complex with cucurbit[7]uril, F432 cage as...

ID or keywords:

Entry

Database: PDB / ID: 8cf6

Title

Dimethylated RSL-R5 in complex with cucurbit[7]uril, F432 cage assembly

Components

RSL-R5

Keywords

SUGAR BINDING PROTEIN / lectin / cucurbituril / biomaterials / supramolecular

Function / homology

methyl alpha-L-fucopyranoside / cucurbit[7]uril

Function and homology information

Biological species

Ralstonia solanacearum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.34 Å

Authors

Ramberg, K. / Crowley, P.B.

Funding support

Ireland, 2items

Citation

Journal: J.Struct.Biol. / Year: 2023
Title: Cage versus sheet: Probing the Determinants of Protein - Cucurbit[7]uril Crystalline Architectures.
Authors: Ramberg, K.O. / Crowley, P.B.

History

Deposition	Feb 2, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 5, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8cf6.cif.gz	79.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8cf6.ent.gz	66.6 KB	Display	PDB format
PDBx/mmJSON format	8cf6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8cf6_validation.pdf.gz	2.3 MB	Display	wwPDB validaton report
Full document	8cf6_full_validation.pdf.gz	2.3 MB	Display
Data in XML	8cf6_validation.xml.gz	17.4 KB	Display
Data in CIF	8cf6_validation.cif.gz	25.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cf/8cf6 ftp://data.pdbj.org/pub/pdb/validation_reports/cf/8cf6	HTTPS FTP

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Related structure data

Related structure data	8cf7C C: citing same article (ref.)
Similar structure data	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	#222 - Jun 2018 Proteins and Nanoparticles similarity (1)

Deposited unit

A: RSL-R5

B: RSL-R5

C: RSL-R5

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: light scattering

Unit cell

Length a, b, c (Å)	200.329, 200.329, 200.329
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	209
Space group name H-M	F432

Components on special symmetry positions

ID	Model	Components
1	1	A-299- HOH
2	1	A-348- HOH
3	1	C-221- HOH
4	1	C-298- HOH
5	1	C-300- HOH

#1: Protein

RSL-R5

Mass: 9844.689 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Ralstonia solanacearum (bacteria) / Production host:

Escherichia coli (E. coli)

#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.: 6 / Source method: obtained synthetically / Formula: C₇H₁₄O₅

#3: Chemical

ChemComp-QQ7 / cucurbit[7]uril

Mass: 1162.962 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄₂H₄₂N₂₈O₁₄ / Feature type: SUBJECT OF INVESTIGATION

#4: Chemical

ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL

Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.84 Å³/Da / Density % sol: 57 % / Description: diamond
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion / Details: 25 % PEG3350 0.1 M Bis-Tris pH 5.5 0.2 M NaCl

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 20, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 1.34→100.17 Å / Num. obs: 77653 / % possible obs: 100 % / Redundancy: 78.2 % / B_iso Wilson estimate: 15.71 Å² / CC_1/2: 0.99 / R_rim(I) all: 0.0137 / Net I/σ(I): 25.7
Reflection shell	Resolution: 1.34→1.36 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3798 / CC_1/2: 0.8 / R_rim(I) all: 0.317 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	v1.17	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.34→45.96 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.59 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2109	3882	5 %
R_work	0.1902	-	-
obs	0.1912	77644	99.99 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.34→45.96 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2088	0	246	376	2710

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	2601
X-RAY DIFFRACTION	f_angle_d	0.872	3705
X-RAY DIFFRACTION	f_dihedral_angle_d	10.985	1029
X-RAY DIFFRACTION	f_chiral_restr	0.084	362
X-RAY DIFFRACTION	f_plane_restr	0.013	554

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 (%)
1.34-1.35	0.3185	117	0.2684	2596	X-RAY DIFFRACTION	100
1.35-1.37	0.2874	138	0.2627	2583	X-RAY DIFFRACTION	100
1.37-1.39	0.2636	124	0.2602	2615	X-RAY DIFFRACTION	100
1.39-1.41	0.2379	125	0.2568	2604	X-RAY DIFFRACTION	100
1.41-1.43	0.2965	143	0.2505	2573	X-RAY DIFFRACTION	100
1.43-1.45	0.2545	126	0.247	2605	X-RAY DIFFRACTION	100
1.45-1.47	0.2984	142	0.2498	2603	X-RAY DIFFRACTION	100
1.47-1.5	0.2829	147	0.236	2585	X-RAY DIFFRACTION	100
1.5-1.52	0.2425	124	0.2291	2594	X-RAY DIFFRACTION	100
1.52-1.55	0.2492	149	0.217	2583	X-RAY DIFFRACTION	100
1.55-1.58	0.2428	131	0.2151	2608	X-RAY DIFFRACTION	100
1.58-1.61	0.2376	161	0.2074	2596	X-RAY DIFFRACTION	100
1.61-1.65	0.2251	137	0.2063	2606	X-RAY DIFFRACTION	100
1.65-1.68	0.2108	138	0.2061	2592	X-RAY DIFFRACTION	100
1.68-1.73	0.2223	147	0.1996	2631	X-RAY DIFFRACTION	100
1.73-1.77	0.2461	127	0.2081	2602	X-RAY DIFFRACTION	100
1.77-1.83	0.2015	142	0.2059	2614	X-RAY DIFFRACTION	100
1.83-1.88	0.206	137	0.1884	2625	X-RAY DIFFRACTION	100
1.88-1.95	0.2145	126	0.1889	2643	X-RAY DIFFRACTION	100
1.95-2.03	0.1885	130	0.1851	2645	X-RAY DIFFRACTION	100
2.03-2.12	0.2126	147	0.1839	2617	X-RAY DIFFRACTION	100
2.12-2.23	0.218	152	0.1867	2640	X-RAY DIFFRACTION	100
2.23-2.37	0.2229	129	0.1927	2675	X-RAY DIFFRACTION	100
2.37-2.56	0.1945	125	0.1948	2678	X-RAY DIFFRACTION	100
2.56-2.81	0.2019	139	0.1859	2686	X-RAY DIFFRACTION	100
2.82-3.22	0.1885	144	0.1774	2711	X-RAY DIFFRACTION	100
3.22-4.06	0.1888	164	0.1576	2728	X-RAY DIFFRACTION	100
4.06-45.96	0.2024	171	0.1768	2924	X-RAY DIFFRACTION	100

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