PDB-7kv5: Surface glycan-binding protein B from Bacteroides fluxus

ID or keywords:

Entry

Database: PDB / ID: 7kv5

Title

Surface glycan-binding protein B from Bacteroides fluxus

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 / DI(HYDROXYETHYL)ETHER / PKD domain protein

Function and homology information

Biological species

Bacteroides fluxus YIT 12057 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.82 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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Download

PDBx/mmCIF format	7kv5.cif.gz	107.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7kv5.ent.gz		Display	PDB format
PDBx/mmJSON format	7kv5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7kv5_validation.pdf.gz	439.5 KB	Display	wwPDB validaton report
Full document	7kv5_full_validation.pdf.gz	439.9 KB	Display
Data in XML	7kv5_validation.xml.gz	14.6 KB	Display
Data in CIF	7kv5_validation.cif.gz	22.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kv/7kv5 ftp://data.pdbj.org/pub/pdb/validation_reports/kv/7kv5	HTTPS FTP

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Related structure data

Related structure data	7kv1C 7kv2C 7kv3C 7kv4C 7kv6C 7kv7C 7kwbC 7kwcC C: citing same article (ref.)
Similar structure data	7kv6-d 1m9c-1 4m6d-2 4dwu-d 6ch5-d 4fh7-d 5chq-d 6ch6-d 6l6q-d 1qvn-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

31.6 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)	59.533, 77.619, 146.621
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	23
Space group name H-M	I222

#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: Chemical	ChemComp-GAI / GUANIDINE Mass: 59.070 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH₅N₃
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.72 Å³/Da / Density % sol: 54.71 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion Details: 0.1 M MES pH6.6, 0.2 M ammonium sulfate, 20 % (w/v) PEG5000MME 0.1 M guanidine hydrochloride

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 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: 0.97946 Å / Relative weight: 1
Reflection	Resolution: 1.82→39.71 Å / Num. obs: 30831 / % possible obs: 99.7 % / Redundancy: 6.6 % / CC_1/2: 0.999 / Net I/σ(I): 12.3
Reflection shell	Resolution: 1.82→1.86 Å / Num. unique obs: 1532 / CC_1/2: 0.934

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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: 1.82→39.709 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.938 / Cross valid method: FREE R-VALUE / ESU R: 0.116 / ESU R Free: 0.117
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2301	1532	4.969 %
R_work	0.1909	29299	-
all	0.193	-	-
obs	-	30831	99.683 %

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: 31.74 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.527 Å²	0 Å²	0 Å²
2-	-	5.096 Å²	0 Å²
3-	-	-	-3.569 Å²

Refinement step

Cycle: LAST / Resolution: 1.82→39.709 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1851	0	30	324	2205

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	1934
X-RAY DIFFRACTION	r_bond_other_d	0.037	0.017	1659
X-RAY DIFFRACTION	r_angle_refined_deg	1.555	1.646	2628
X-RAY DIFFRACTION	r_angle_other_deg	2.443	1.574	3862
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.558	5	245
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.022	25	84
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.026	10	4
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.623	15	270
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.565	15	2
X-RAY DIFFRACTION	r_chiral_restr	0.069	0.2	253
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	2205
X-RAY DIFFRACTION	r_gen_planes_other	0.011	0.02	397
X-RAY DIFFRACTION	r_nbd_refined	0.198	0.2	326
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.216	0.2	1562
X-RAY DIFFRACTION	r_nbtor_refined	0.172	0.2	911
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	788
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.187	0.2	232
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.002	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.065	0.2	5
X-RAY DIFFRACTION	r_nbd_other	0.161	0.2	23
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.219	0.2	20
X-RAY DIFFRACTION	r_mcbond_it	2.445	3.265	986
X-RAY DIFFRACTION	r_mcbond_other	2.44	3.262	985
X-RAY DIFFRACTION	r_mcangle_it	3.25	4.87	1229
X-RAY DIFFRACTION	r_mcangle_other	3.251	4.873	1230
X-RAY DIFFRACTION	r_scbond_it	3.283	3.415	948
X-RAY DIFFRACTION	r_scbond_other	3.281	3.419	949
X-RAY DIFFRACTION	r_scangle_it	4.559	5.029	1399
X-RAY DIFFRACTION	r_scangle_other	4.557	5.031	1400
X-RAY DIFFRACTION	r_lrange_it	5.876	38.49	2203
X-RAY DIFFRACTION	r_lrange_other	5.875	38.505	2204

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
1.82-1.867	0.349	106	0.323	2137	0.324	2253	0.47	0.44	99.5561	0.302
1.867-1.918	0.325	115	0.301	2085	0.302	2209	0.669	0.646	99.5926	0.277
1.918-1.974	0.261	116	0.259	1987	0.259	2110	0.771	0.764	99.6682	0.232
1.974-2.034	0.212	89	0.238	1997	0.237	2090	0.823	0.823	99.8086	0.219
2.034-2.101	0.258	98	0.225	1923	0.226	2023	0.852	0.861	99.9011	0.208
2.101-2.174	0.238	92	0.201	1825	0.203	1922	0.872	0.899	99.7399	0.184
2.174-2.256	0.23	85	0.182	1822	0.184	1907	0.896	0.924	100	0.168
2.256-2.348	0.219	91	0.175	1703	0.177	1805	0.928	0.936	99.3906	0.161
2.348-2.452	0.269	84	0.169	1671	0.174	1757	0.902	0.941	99.8862	0.16
2.452-2.571	0.258	77	0.164	1579	0.169	1656	0.921	0.95	100	0.155
2.571-2.71	0.233	75	0.172	1532	0.175	1610	0.929	0.944	99.8137	0.164
2.71-2.873	0.229	71	0.179	1428	0.181	1503	0.935	0.945	99.7339	0.173
2.873-3.07	0.243	73	0.18	1330	0.183	1412	0.93	0.948	99.3626	0.178
3.07-3.315	0.238	81	0.195	1261	0.197	1345	0.935	0.945	99.777	0.197
3.315-3.629	0.227	55	0.181	1169	0.183	1228	0.943	0.963	99.6743	0.187
3.629-4.053	0.16	65	0.168	1063	0.168	1128	0.961	0.966	100	0.178
4.053-4.671	0.167	55	0.136	938	0.138	997	0.967	0.975	99.5988	0.153
4.671-5.702	0.235	43	0.162	808	0.166	852	0.942	0.965	99.8826	0.182
5.702-7.981	0.26	35	0.249	650	0.249	686	0.919	0.937	99.8542	0.271
7.981-39.709	0.253	26	0.234	391	0.235	424	0.914	0.938	98.3491	0.273

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