PDB-7kv6: Surface glycan-binding protein B from Bacteroides fluxus in compl...

ID or keywords:

Entry

Database: PDB / ID: 7kv6

Title

Surface glycan-binding protein B from Bacteroides fluxus in complex with mixed-linkage glucotriose

Components

PKD domain protein

Keywords

SUGAR BINDING PROTEIN / CBM / lectin

Function / homology

PKD domain / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like fold / GUANIDINE / PKD domain protein

Function and homology information

Biological species

Bacteroides fluxus YIT 12057 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.6 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 26, 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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PDBx/mmCIF format	7kv6.cif.gz	110.8 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kv/7kv6 ftp://data.pdbj.org/pub/pdb/validation_reports/kv/7kv6	HTTPS FTP

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Related structure data

Related structure data	7kv1C 7kv2C 7kv3C 7kv4C 7kv5C 7kv7C 7kwbC 7kwcC C: citing same article (ref.)
Similar structure data	7kv5-d 3ord-d 4fh6-d 4fh7-d 4jyq-d 4dwu-d 2zbq-d 1qvn-1 3ok5-d 1m9c-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
Related items in Molecule of the Month	#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

AAA: PKD domain protein

hetero molecules

31.8 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)	59.980, 77.222, 148.379
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	23
Space group name H-M	I222

Components on special symmetry positions

ID	Model	Components
1	1	AAA-1360- HOH

#1: Protein

PKD domain protein

Mass: 31185.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bacteroides fluxus YIT 12057 (bacteria)
Gene: HMPREF9446_00613 / Production host:

Escherichia coli (E. coli) / References: UniProt: F3PPH3

#2: Polysaccharide

beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose

Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DGlcpb1-4DGlcpb1-3DGlcpb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5]/1-1-1/a3-b1_b4-c1	WURCS	PDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}	LINUCS	PDB-CARE

#3: Chemical

ChemComp-GAI / GUANIDINE

Mass: 59.070 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH₅N₃

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.75 Å³/Da / Density % sol: 55.35 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion Details: 0.1 M MES pH6.6, 0.2 M ammonium sulfate, 20 % (w/v) PEG5000MME, 0.1M guanidine hydrochloride

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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: 0.9795 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 18, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.6→74.19 Å / Num. obs: 43047 / % possible obs: 95.5 % / Redundancy: 11.8 % / CC_1/2: 0.999 / Net I/σ(I): 34.4
Reflection shell	Resolution: 1.61→1.64 Å / Num. unique obs: 2197 / CC_1/2: 0.907

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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: 1.6→74.189 Å / Cor.coef. F_o:F_c: 0.971 / Cor.coef. F_o:F_c free: 0.967 / Cross valid method: FREE R-VALUE / ESU R: 0.08 / ESU R Free: 0.081
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2043	2197	5.104 %
R_work	0.1782	40850	-
all	0.18	-	-
obs	-	43047	95.437 %

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: 31.631 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.937 Å²	0 Å²	0 Å²
2-	-	3.521 Å²	0 Å²
3-	-	-	-2.584 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→74.189 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1907	0	42	331	2280

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.013	2020
X-RAY DIFFRACTION	r_bond_other_d	0.037	0.017	1703
X-RAY DIFFRACTION	r_angle_refined_deg	1.729	1.669	2759
X-RAY DIFFRACTION	r_angle_other_deg	2.464	1.595	3968
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.333	5	257
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.727	25.057	87
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.028	10	2
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.218	15	272
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.674	15	2
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	277
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	2298
X-RAY DIFFRACTION	r_gen_planes_other	0.014	0.02	412
X-RAY DIFFRACTION	r_nbd_refined	0.203	0.2	321
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.221	0.2	1533
X-RAY DIFFRACTION	r_nbtor_refined	0.177	0.2	975
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	823
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.168	0.2	230
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.155	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.164	0.2	4
X-RAY DIFFRACTION	r_nbd_other	0.192	0.2	19
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.12	0.2	20
X-RAY DIFFRACTION	r_mcbond_it	2.588	3.228	1027
X-RAY DIFFRACTION	r_mcbond_other	2.559	3.225	1026
X-RAY DIFFRACTION	r_mcangle_it	3.254	4.831	1284
X-RAY DIFFRACTION	r_mcangle_other	3.264	4.833	1285
X-RAY DIFFRACTION	r_scbond_it	3.776	3.405	993
X-RAY DIFFRACTION	r_scbond_other	3.775	3.405	993
X-RAY DIFFRACTION	r_scangle_it	5.235	5.011	1475
X-RAY DIFFRACTION	r_scangle_other	5.233	5.011	1476
X-RAY DIFFRACTION	r_lrange_it	6.521	39.439	2282
X-RAY DIFFRACTION	r_lrange_other	6.294	38.158	2191

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.609-1.651	0.305	107	0.309	2194	0.309	3282	0.711	0.684	70.1097	0.28
1.651-1.696	0.332	115	0.316	2517	0.317	3206	0.596	0.64	82.0961	0.28
1.696-1.745	0.331	163	0.27	2717	0.273	3137	0.741	0.791	91.8075	0.23
1.745-1.799	0.282	156	0.242	2791	0.244	3018	0.849	0.861	97.6474	0.205
1.799-1.858	0.237	153	0.209	2796	0.211	2957	0.899	0.914	99.7295	0.18
1.858-1.923	0.224	127	0.194	2721	0.195	2861	0.922	0.936	99.5456	0.163
1.923-1.996	0.221	150	0.194	2591	0.196	2751	0.923	0.931	99.6365	0.166
1.996-2.077	0.233	121	0.192	2521	0.194	2659	0.92	0.937	99.3607	0.166
2.077-2.169	0.241	131	0.184	2407	0.187	2550	0.924	0.941	99.5294	0.166
2.169-2.275	0.214	126	0.175	2319	0.177	2452	0.944	0.952	99.7145	0.158
2.275-2.398	0.19	130	0.163	2187	0.165	2324	0.952	0.958	99.6988	0.151
2.398-2.543	0.248	127	0.175	2031	0.18	2194	0.934	0.95	98.3592	0.164
2.543-2.719	0.19	103	0.172	1979	0.173	2088	0.952	0.955	99.7126	0.168
2.719-2.936	0.197	82	0.167	1844	0.168	1928	0.953	0.96	99.8963	0.171
2.936-3.216	0.196	86	0.165	1702	0.167	1795	0.956	0.96	99.61	0.176
3.216-3.595	0.179	87	0.166	1528	0.167	1627	0.966	0.967	99.2624	0.182
3.595-4.149	0.174	82	0.16	1361	0.161	1449	0.969	0.968	99.5859	0.187
4.149-5.078	0.162	73	0.142	1163	0.143	1243	0.973	0.976	99.4368	0.177
5.078-7.164	0.244	46	0.191	937	0.194	986	0.947	0.962	99.6957	0.239
7.164-74.189	0.197	32	0.211	543	0.21	590	0.961	0.947	97.4576	0.313

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