PDB-7kwc: Surface glycan-binding protein B (truncated) from Bacteroides the...

ID or keywords:

Entry

Database: PDB / ID: 7kwc

Title

Surface glycan-binding protein B (truncated) from Bacteroides thetaiotaomicron

Components

BtSGBP-B_31-285

Keywords

SUGAR BINDING PROTEIN / CBM / lectin

Function / homology

PKD domain superfamily / Galactose-binding-like domain superfamily / DUF5017 domain-containing protein

Function and homology information

Biological species

Bacteroides thetaiotaomicron (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.611 Å

Authors

Tamura, K. / Brumer, H. / Van Petegem, F.

Funding support

Canada, 1items

Citation

Journal: J.Biol.Chem. / Year: 2021
Title: Distinct protein architectures mediate species-specific beta-glucan binding and metabolism in the human gut microbiota.
Authors: Tamura, K. / Dejean, G. / Van Petegem, F. / Brumer, H.

History

Deposition	Nov 30, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 17, 2021	Provider: repository / Type: Initial release
Revision 1.1	Mar 3, 2021	Group: Database references / Category: citation Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Jul 21, 2021	Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3	Mar 6, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7kwc.cif.gz	96.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7kwc.ent.gz		Display	PDB format
PDBx/mmJSON format	7kwc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7kwc_validation.pdf.gz	421.7 KB	Display	wwPDB validaton report
Full document	7kwc_full_validation.pdf.gz	422.7 KB	Display
Data in XML	7kwc_validation.xml.gz	10.2 KB	Display
Data in CIF	7kwc_validation.cif.gz	12.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kw/7kwc ftp://data.pdbj.org/pub/pdb/validation_reports/kw/7kwc	HTTPS FTP

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Related structure data

Related structure data	7kv1C 7kv2C 7kv3C 7kv4C 7kv5C 7kv6C 7kv7C 7kwbC C: citing same article (ref.)
Similar structure data	4mzg-2 5mkg-2 4tnn-d 4lsd-1 5vbb-d 5b3i-1 3aqf-d 5mkg-1 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

Deposited unit

AAA: BtSGBP-B_31-285

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	80.689, 80.689, 86.027
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

#1: Protein	BtSGBP-B_31-285 Mass: 31663.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Gene: HMPREF2534_00387 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A139L065
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.21 Å³/Da / Density % sol: 44.37 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion Details: 0.1M magnesium chloride, 0.1M sodium citrate, 15% (w/v) PEG4000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 30, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97946 Å / Relative weight: 1
Reflection	Resolution: 2.61→19.64 Å / Num. obs: 8556 / % possible obs: 94.5 % / Redundancy: 25.4 % / CC_1/2: 1 / Net I/σ(I): 42.5
Reflection shell	Resolution: 2.61→2.66 Å / Num. unique obs: 416 / CC_1/2: 0.951

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.611→19.64 Å / Cor.coef. F_o:F_c: 0.928 / Cor.coef. F_o:F_c free: 0.902 / Cross valid method: FREE R-VALUE / ESU R: 1.15 / ESU R Free: 0.38
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2922	414	4.839 %
R_work	0.2501	8142	-
all	0.252	-	-
obs	-	8556	94.084 %

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: 53.316 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.844 Å²	0 Å²	0 Å²
2-	-	1.844 Å²	0 Å²
3-	-	-	-3.688 Å²

Refinement step

Cycle: LAST / Resolution: 2.611→19.64 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1861	0	0	12	1873

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.001	0.013	1910
X-RAY DIFFRACTION	r_bond_other_d	0.037	0.017	1640
X-RAY DIFFRACTION	r_angle_refined_deg	1.181	1.642	2615
X-RAY DIFFRACTION	r_angle_other_deg	2.433	1.57	3807
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.331	5	242
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.05	24.767	86
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.941	15	271
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	7.705	15	3
X-RAY DIFFRACTION	r_chiral_restr	0.025	0.2	268
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	2170
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	395
X-RAY DIFFRACTION	r_nbd_refined	0.145	0.2	240
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.184	0.2	1411
X-RAY DIFFRACTION	r_nbtor_refined	0.154	0.2	908
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.064	0.2	722
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.128	0.2	38
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.122	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.12	0.2	9
X-RAY DIFFRACTION	r_nbd_other	0.141	0.2	26
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.038	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	0.807	6.004	974
X-RAY DIFFRACTION	r_mcbond_other	0.806	6.003	973
X-RAY DIFFRACTION	r_mcangle_it	1.491	9.002	1214
X-RAY DIFFRACTION	r_mcangle_other	1.491	9.002	1215
X-RAY DIFFRACTION	r_scbond_it	0.478	5.898	936
X-RAY DIFFRACTION	r_scbond_other	0.477	5.899	937
X-RAY DIFFRACTION	r_scangle_it	0.908	8.854	1401
X-RAY DIFFRACTION	r_scangle_other	0.907	8.855	1402
X-RAY DIFFRACTION	r_lrange_it	2.195	66.11	1925
X-RAY DIFFRACTION	r_lrange_other	2.194	66.1	1926

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 (%)
2.611-2.678	0.331	28	0.359	388	X-RAY DIFFRACTION	63.6086
2.678-2.752	0.441	30	0.335	527	X-RAY DIFFRACTION	88.6943
2.752-2.831	0.322	34	0.339	578	X-RAY DIFFRACTION	100
2.831-2.918	0.308	26	0.315	587	X-RAY DIFFRACTION	100
2.918-3.013	0.291	38	0.295	549	X-RAY DIFFRACTION	100
3.013-3.119	0.411	34	0.299	537	X-RAY DIFFRACTION	100
3.119-3.236	0.26	27	0.298	523	X-RAY DIFFRACTION	100
3.236-3.368	0.339	16	0.288	515	X-RAY DIFFRACTION	100
3.368-3.517	0.355	18	0.287	372	X-RAY DIFFRACTION	77.381
3.517-3.688	0.284	23	0.291	429	X-RAY DIFFRACTION	90.4
3.688-3.887	0.268	24	0.25	439	X-RAY DIFFRACTION	99.1435
3.887-4.122	0.284	30	0.22	377	X-RAY DIFFRACTION	93.135
4.122-4.405	0.574	9	0.215	415	X-RAY DIFFRACTION	100
4.405-4.755	0.195	14	0.213	394	X-RAY DIFFRACTION	100
4.755-5.206	0.231	14	0.192	341	X-RAY DIFFRACTION	100
5.206-5.815	0.208	20	0.216	316	X-RAY DIFFRACTION	100
5.815-6.703	0.313	4	0.263	299	X-RAY DIFFRACTION	100
6.703-8.183	0.265	7	0.249	253	X-RAY DIFFRACTION	100
8.183-11.463	0.331	15	0.184	201	X-RAY DIFFRACTION	100
11.463-19.64	0.2	3	0.2	102	X-RAY DIFFRACTION	77.2059

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