PDB-9bal: Surface glycan-binding protein A (SGBP-A, SusD-like) from a mixed...

ID or keywords:

Entry

Database: PDB / ID: 9bal

Title

Surface glycan-binding protein A (SGBP-A, SusD-like) from a mixed-linkage beta-glucan utilization locus in Segatella copri in complex with cellopentaose

Components

Surface glycan-binding protein A (SGBP-A)

Keywords

SUGAR BINDING PROTEIN / glycan-binding protein / SGBP-A / mixed-linkage beta-glucan / cellopentaose

Function / homology

SusD-like 2 / Starch-binding associating with outer membrane / Tetratricopeptide-like helical domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / beta-cellopentaose / Uncharacterized protein

Function and homology information

Biological species

Segatella copri DSM 18205 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Cordeiro, R.L. / Golisch, B. / Brumer, H. / Van Petegem, F.

Funding support

Canada, 1items

Citation

Journal: J.Biol.Chem. / Year: 2024
Title: The molecular basis of cereal mixed-linkage beta-glucan utilization by the human gut bacterium Segatella copri.
Authors: Golisch, B. / Cordeiro, R.L. / Fraser, A.S.C. / Briggs, J. / Stewart, W.A. / Van Petegem, F. / Brumer, H.

History

Deposition	Apr 4, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 9, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9bal.cif.gz	311.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9bal.ent.gz	206.5 KB	Display	PDB format
PDBx/mmJSON format	9bal.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9bal_validation.pdf.gz	963.6 KB	Display	wwPDB validaton report
Full document	9bal_full_validation.pdf.gz	964.5 KB	Display
Data in XML	9bal_validation.xml.gz	28.9 KB	Display
Data in CIF	9bal_validation.cif.gz	42.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ba/9bal ftp://data.pdbj.org/pub/pdb/validation_reports/ba/9bal	HTTPS FTP

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Related structure data

Related structure data	9bamC 9bjxC 9bmkC 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	#254 - Feb 2021 Cellulose Synthase similarity (1) #261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: Surface glycan-binding protein A (SGBP-A)

hetero molecules

65.6 kDa, 1 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)	68.960, 77.410, 100.090
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein

Surface glycan-binding protein A (SGBP-A)

Mass: 64702.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Segatella copri DSM 18205 (bacteria) / Gene: PREVCOP_05098 / Production host:

Escherichia coli BL21 (bacteria) / References: UniProt: D1PD12

#2: Polysaccharide

beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D- ...

Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 828.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellopentaose

Descriptor	Type	Program
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,5,4/[a2122h-1b_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1	WURCS	PDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}}	LINUCS	PDB-CARE

#3: Chemical

ChemComp-MG / MAGNESIUM ION

Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 495 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

Y

Has protein modification

N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.06 Å³/Da / Density % sol: 40.42 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris-HCl (pH 8.5) and 23% (w/v) Polyethylene glycol (PEG) 8,000 Temp details: Room temperature

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.95372 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 3, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95372 Å / Relative weight: 1
Reflection	Resolution: 1.5→42.03 Å / Num. obs: 86193 / % possible obs: 99.84 % / Redundancy: 2 % / B_iso Wilson estimate: 16.23 Å² / CC_1/2: 1 / CC star: 1 / R_merge(I) obs: 0.01551 / Net I/σ(I): 18.83
Reflection shell	Resolution: 1.5→1.554 Å / R_merge(I) obs: 0.1393 / Num. unique obs: 8470 / CC_1/2: 0.94

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.5→42.03 Å / SU ML: 0.118 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.951
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1667	4307	5 %
R_work	0.1493	81868	-
obs	0.1502	86175	99.84 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 19.87 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→42.03 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4412	0	57	497	4966

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0059	4760
X-RAY DIFFRACTION	f_angle_d	0.9696	6501
X-RAY DIFFRACTION	f_chiral_restr	0.053	704
X-RAY DIFFRACTION	f_plane_restr	0.0086	847
X-RAY DIFFRACTION	f_dihedral_angle_d	5.7251	661

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 (%)
1.5-1.52	0.2116	140	0.1784	2666	X-RAY DIFFRACTION	99.96
1.52-1.53	0.1889	144	0.1635	2726	X-RAY DIFFRACTION	99.86
1.53-1.55	0.1559	139	0.1557	2655	X-RAY DIFFRACTION	99.86
1.55-1.57	0.1931	144	0.1522	2721	X-RAY DIFFRACTION	99.86
1.57-1.59	0.1784	141	0.1566	2685	X-RAY DIFFRACTION	100
1.59-1.62	0.1764	144	0.1562	2730	X-RAY DIFFRACTION	99.97
1.62-1.64	0.2078	142	0.1522	2698	X-RAY DIFFRACTION	99.89
1.64-1.66	0.1965	141	0.1526	2676	X-RAY DIFFRACTION	100
1.66-1.69	0.1804	143	0.1517	2721	X-RAY DIFFRACTION	99.9
1.69-1.72	0.2044	142	0.1459	2709	X-RAY DIFFRACTION	99.96
1.72-1.75	0.1824	142	0.1585	2689	X-RAY DIFFRACTION	100
1.75-1.78	0.161	143	0.159	2721	X-RAY DIFFRACTION	99.97
1.78-1.81	0.1898	143	0.1589	2724	X-RAY DIFFRACTION	100
1.81-1.85	0.1719	143	0.1579	2702	X-RAY DIFFRACTION	99.93
1.85-1.89	0.1799	144	0.1569	2735	X-RAY DIFFRACTION	99.93
1.89-1.93	0.208	142	0.1492	2696	X-RAY DIFFRACTION	100
1.93-1.98	0.1754	141	0.1541	2709	X-RAY DIFFRACTION	99.86
1.98-2.04	0.1683	145	0.1509	2744	X-RAY DIFFRACTION	100
2.04-2.1	0.1674	143	0.1487	2724	X-RAY DIFFRACTION	100
2.1-2.16	0.1597	144	0.1518	2728	X-RAY DIFFRACTION	100
2.16-2.24	0.1704	143	0.1453	2717	X-RAY DIFFRACTION	100
2.24-2.33	0.1759	144	0.15	2741	X-RAY DIFFRACTION	100
2.33-2.44	0.1528	144	0.1514	2739	X-RAY DIFFRACTION	100
2.44-2.56	0.1693	144	0.1531	2739	X-RAY DIFFRACTION	99.97
2.56-2.73	0.1831	145	0.1612	2758	X-RAY DIFFRACTION	100
2.73-2.94	0.1759	146	0.1599	2762	X-RAY DIFFRACTION	99.97
2.94-3.23	0.1614	147	0.158	2789	X-RAY DIFFRACTION	99.93
3.23-3.7	0.1605	146	0.1432	2782	X-RAY DIFFRACTION	99.93
3.7-4.66	0.1298	148	0.1245	2816	X-RAY DIFFRACTION	100
4.66-42.03	0.1574	150	0.1454	2866	X-RAY DIFFRACTION	97.04

Refinement TLS params.

Method: refined / Origin x: -17.0281429102 Å / Origin y: 16.6401230054 Å / Origin z: -21.7522585471 Å

	11	12	13	21	22	23	31	32	33
T	0.0981057535367 Å²	-0.00338376317446 Å²	0.00765629204041 Å²	-	0.104063276002 Å²	0.0133477676806 Å²	-	-	0.114796977437 Å²
L	0.571116586354 °²	0.0930545762516 °²	0.144219921928 °²	-	0.425890801024 °²	0.107228210382 °²	-	-	0.485427243934 °²
S	0.0336975986867 Å °	-0.0237443303421 Å °	-0.00380730487743 Å °	0.0177761901598 Å °	-0.0320120638137 Å °	-0.0384354195683 Å °	-0.018197088067 Å °	0.0585702808897 Å °	-0.00165756646202 Å °

Refinement TLS group

Selection details: all

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