PDB-8s5b: Crystal structure of the sulfoquinovosyl binding protein (SmoF) f...

ID or keywords:

Entry

Database: PDB / ID: 8s5b

Title

Crystal structure of the sulfoquinovosyl binding protein (SmoF) from A. tumefaciens sulfo-SMO pathway in complex with SQOctyl ligand

Components

Sulfoquinovosyl glycerol-binding protein SmoF

Keywords

SUGAR BINDING PROTEIN / agrobacterium tumefaciens / sulfoquinovose / sulfosugar / solute binding protein / sulfoglycolysis / sulfo-SMO pathway

Function / homology

Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / periplasmic space / : / Sulfoquinovosyl glycerol-binding protein SmoF

Function and homology information

Biological species

Agrobacterium tumefaciens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Snow, A.J.D. / Sharma, M. / Davies, G.J.

Funding support

United Kingdom, 2items

Citation

Journal: Org.Biomol.Chem. / Year: 2024
Title: Capture-and-release of a sulfoquinovose-binding protein on sulfoquinovose-modified agarose.
Authors: Arumapperuma, T. / Snow, A.J.D. / Lee, M. / Sharma, M. / Zhang, Y. / Lingford, J.P. / Goddard-Borger, E.D. / Davies, G.J. / Williams, S.J.

History

Deposition	Feb 23, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 17, 2024	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2024	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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8s5b.cif.gz	157.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8s5b.ent.gz		Display	PDB format
PDBx/mmJSON format	8s5b.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8s5b_validation.pdf.gz	709.7 KB	Display	wwPDB validaton report
Full document	8s5b_full_validation.pdf.gz	710.8 KB	Display
Data in XML	8s5b_validation.xml.gz	17.5 KB	Display
Data in CIF	8s5b_validation.cif.gz	26 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s5/8s5b ftp://data.pdbj.org/pub/pdb/validation_reports/s5/8s5b	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#205 - Jan 2017 Nuclear Pore Complex similarity (2) #221 - May 2018 Human Papillomavirus and Vaccines similarity (2) #243 - Mar 2020 Voltage-gated Sodium Channels similarity (2)

Deposited unit

A: Sulfoquinovosyl glycerol-binding protein SmoF

hetero molecules

44.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	53.777, 65.851, 107.018
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Sulfoquinovosyl glycerol-binding protein SmoF / SQGro-binding protein SmoF / SQ monooxygenase cluster protein F Mass: 44074.840 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Gene: smoF, Atu3282 / Production host: Escherichia coli (E. coli) / References: UniProt: A9CEY9
#2: Chemical	ChemComp-A1H5E / [(2~{S},3~{S},4~{S},5~{R},6~{S})-6-octoxy-3,4,5-tris(oxidanyl)oxan-2-yl]methanesulfonic acid Mass: 356.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₄H₂₈O₈S / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.15 Å³/Da / Density % sol: 42.78 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 200 mM calcium acetate, 100 mM Bis-TRIS pH 6.5, 25% w/v PEG 2000 MME, 1:1 protein:mother liquor ratio with SmoF at 50mg/ml in 50mM TRIS, 300mM NaCl pH 7.5

-
Data collection

Diffraction

Mean temperature: 120 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I03 / Wavelength: 0.9763 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 15, 2019

Radiation

Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9763 Å / Relative weight: 1

Reflection

Resolution: 1.8→56.147 Å / Num. obs: 36036 / % possible obs: 100 % / Redundancy: 8 % / CC_1/2: 0.965 / R_merge(I) obs: 0.116 / R_pim(I) all: 0.065 / R_rim(I) all: 0.134 / Net I/σ(I): 10.1

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all
9-56.08	6.2	0.104	352	0.814	0.062	0.122
1.8-1.84	7.9	0.47	2098	0.952	0.262	0.54

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.8→56.147 Å / Cor.coef. F_o:F_c: 0.924 / Cor.coef. F_o:F_c free: 0.9 / SU B: 4 / SU ML: 0.123 / Cross valid method: FREE R-VALUE / ESU R: 0.157 / ESU R Free: 0.15
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2716	1842	5.122 %
R_work	0.2255	34124	-
all	0.228	-	-
obs	-	35966	99.939 %

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: 19.01 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.167 Å²	0 Å²	-0 Å²
2-	-	-0.187 Å²	0 Å²
3-	-	-	3.355 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→56.147 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2838	0	23	243	3104

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	2935
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2702
X-RAY DIFFRACTION	r_angle_refined_deg	1.552	1.641	4002
X-RAY DIFFRACTION	r_angle_other_deg	1.384	1.578	6226
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.136	5	378
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.487	24.597	124
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.497	15	453
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.493	15	7
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	397
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	3336
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	634
X-RAY DIFFRACTION	r_nbd_refined	0.205	0.2	601
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.174	0.2	2502
X-RAY DIFFRACTION	r_nbtor_refined	0.167	0.2	1434
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	1271
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.144	0.2	210
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.192	0.2	3
X-RAY DIFFRACTION	r_nbd_other	0.171	0.2	31
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.224	0.2	9
X-RAY DIFFRACTION	r_mcbond_it	1.385	1.97	1512
X-RAY DIFFRACTION	r_mcbond_other	1.376	1.969	1511
X-RAY DIFFRACTION	r_mcangle_it	1.976	2.948	1887
X-RAY DIFFRACTION	r_mcangle_other	1.976	2.949	1888
X-RAY DIFFRACTION	r_scbond_it	1.744	2.075	1423
X-RAY DIFFRACTION	r_scbond_other	1.744	2.074	1424
X-RAY DIFFRACTION	r_scangle_it	2.614	3.051	2114
X-RAY DIFFRACTION	r_scangle_other	2.613	3.051	2115
X-RAY DIFFRACTION	r_lrange_it	3.792	23.656	3363
X-RAY DIFFRACTION	r_lrange_other	3.735	23.452	3324

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 (%)
1.8-1.847	0.291	138	0.26	2495	X-RAY DIFFRACTION	99.8862
1.847-1.897	0.275	130	0.256	2406	X-RAY DIFFRACTION	99.9606
1.897-1.952	0.367	133	0.322	2339	X-RAY DIFFRACTION	99.8788
1.952-2.012	0.292	127	0.229	2275	X-RAY DIFFRACTION	100
2.012-2.078	0.297	122	0.212	2240	X-RAY DIFFRACTION	100
2.078-2.151	0.239	125	0.22	2159	X-RAY DIFFRACTION	100
2.151-2.232	0.282	106	0.233	2087	X-RAY DIFFRACTION	99.7725
2.232-2.324	0.333	125	0.296	1976	X-RAY DIFFRACTION	99.9524
2.324-2.427	0.257	94	0.195	1944	X-RAY DIFFRACTION	100
2.427-2.545	0.224	110	0.184	1835	X-RAY DIFFRACTION	100
2.545-2.683	0.291	98	0.207	1763	X-RAY DIFFRACTION	100
2.683-2.845	0.307	89	0.211	1673	X-RAY DIFFRACTION	100
2.845-3.042	0.275	74	0.213	1583	X-RAY DIFFRACTION	100
3.042-3.285	0.273	62	0.229	1476	X-RAY DIFFRACTION	100
3.285-3.598	0.267	78	0.228	1372	X-RAY DIFFRACTION	100
3.598-4.023	0.252	65	0.222	1238	X-RAY DIFFRACTION	100
4.023-4.644	0.244	44	0.197	1112	X-RAY DIFFRACTION	100
4.644-5.685	0.264	49	0.202	961	X-RAY DIFFRACTION	100
5.685-8.028	0.231	42	0.203	749	X-RAY DIFFRACTION	100
8.028-56.147	0.215	31	0.265	441	X-RAY DIFFRACTION	99.7886

-
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