PDB-7vet: Crystal structure of bacterial chemotaxis-dependent pectin-bindin...

ID or keywords:

Entry

Database: PDB / ID: 7vet

Title

Crystal structure of bacterial chemotaxis-dependent pectin-binding protein SPH1118 in a closed conformation

Components

SPH1118

Keywords

SUGAR BINDING PROTEIN / pectin-binding protein / chemotaxis / gram-negative bacteria

Biological species

Sphingomonas sp. A1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.25 Å

Authors

Anamizu, K. / Takase, R. / Hio, M. / Watanebe, D. / Mikami, B. / Hashimoto, W.

Funding support

Japan, 1items

Citation

Journal: Sci Rep / Year: 2022
Title: Substrate size-dependent conformational changes of bacterial pectin-binding protein crucial for chemotaxis and assimilation.
Authors: Anamizu, K. / Takase, R. / Hio, M. / Watanabe, D. / Mikami, B. / Hashimoto, W.

History

Deposition	Sep 10, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 17, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7vet.cif.gz	250.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7vet.ent.gz	199.6 KB	Display	PDB format
PDBx/mmJSON format	7vet.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7vet_validation.pdf.gz	434.9 KB	Display	wwPDB validaton report
Full document	7vet_full_validation.pdf.gz	440.5 KB	Display
Data in XML	7vet_validation.xml.gz	41.9 KB	Display
Data in CIF	7vet_validation.cif.gz	58.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ve/7vet ftp://data.pdbj.org/pub/pdb/validation_reports/ve/7vet	HTTPS FTP

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Related structure data

Related structure data	7veqC 7verC 7veuC 7vevSC 7vewC C: citing same article (ref.) S: Starting model for refinement

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: SPH1118

B: SPH1118

140 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: SPH1118

defined by author
Evidence: gel filtration
70.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: SPH1118

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

Unit cell

Length a, b, c (Å)	50.626, 54.998, 112.829
Angle α, β, γ (deg.)	103.034, 97.400, 92.360
Int Tables number	1
Space group name H-M	P1

#1: Protein	SPH1118 Mass: 70050.602 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphingomonas sp. A1 (bacteria) / Production host: Escherichia coli (E. coli)
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.16 Å³/Da / Density % sol: 43.07 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20% PEG3350 0.2 M Ammonium formate 0.0209 mM Polygalacturonic acid sodium

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 18, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.25→48.2 Å / Num. obs: 53456 / % possible obs: 95.9 % / Redundancy: 6.12 % / R_merge(I) obs: 0.055 / Net I/σ(I): 14.2
Reflection shell	Resolution: 2.25→2.39 Å / R_merge(I) obs: 0.109 / Num. unique obs: 8527

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
XDS		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7VEV

7vev

Resolution: 2.25→43.53 Å / Cor.coef. F_o:F_c: 0.928 / Cor.coef. F_o:F_c free: 0.893 / Cross valid method: FREE R-VALUE / ESU R: 0.456 / ESU R Free: 0.257
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2512	2673	5 %
R_work	0.2089	50783	-
all	0.211	-	-
obs	-	53456	95.957 %

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: 28.387 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.471 Å²	-1.812 Å²	-0.299 Å²
2-	-	-2.102 Å²	0.29 Å²
3-	-	-	2.317 Å²

Refinement step

Cycle: LAST / Resolution: 2.25→43.53 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9692	0	0	186	9878

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.013	9959
X-RAY DIFFRACTION	r_bond_other_d	0.034	0.017	9437
X-RAY DIFFRACTION	r_angle_refined_deg	1.79	1.648	13533
X-RAY DIFFRACTION	r_angle_other_deg	2.24	1.58	21748
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.204	5	1222
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.332	22.773	512
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.111	15	1701
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.146	15	58
X-RAY DIFFRACTION	r_chiral_restr	0.104	0.2	1269
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	11320
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	2332
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.2	1979
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.222	0.2	9052
X-RAY DIFFRACTION	r_nbtor_refined	0.185	0.2	4992
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.074	0.2	4791
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.153	0.2	309
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.13	0.2	7
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.116	0.2	22
X-RAY DIFFRACTION	r_nbd_other	0.32	0.2	78
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.206	0.2	11
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.129	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	4.301	2.992	4885
X-RAY DIFFRACTION	r_mcbond_other	4.301	2.992	4884
X-RAY DIFFRACTION	r_mcangle_it	5.011	4.471	6108
X-RAY DIFFRACTION	r_mcangle_other	5.011	4.472	6109
X-RAY DIFFRACTION	r_scbond_it	5.593	3.085	5074
X-RAY DIFFRACTION	r_scbond_other	5.592	3.085	5074
X-RAY DIFFRACTION	r_scangle_it	6.289	4.518	7425
X-RAY DIFFRACTION	r_scangle_other	6.289	4.518	7426
X-RAY DIFFRACTION	r_lrange_it	6.314	33.786	11180
X-RAY DIFFRACTION	r_lrange_other	6.318	33.792	11154

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
2.25-2.308	0.316	191	0.244	3627	0.248	4199	0.857	0.884	90.9264	0.222
2.308-2.371	0.319	191	0.228	3634	0.232	3938	0.856	0.894	97.1305	0.212
2.371-2.44	0.29	190	0.233	3606	0.235	3917	0.869	0.88	96.9109	0.221
2.44-2.515	0.315	185	0.229	3518	0.234	3811	0.859	0.884	97.1661	0.217
2.515-2.597	0.313	174	0.234	3317	0.238	3607	0.877	0.889	96.784	0.227
2.597-2.688	0.303	171	0.224	3237	0.228	3546	0.857	0.885	96.1083	0.217
2.688-2.789	0.257	166	0.224	3166	0.226	3441	0.885	0.896	96.8323	0.219
2.789-2.902	0.283	160	0.218	3028	0.222	3306	0.893	0.911	96.4307	0.219
2.902-3.03	0.241	152	0.218	2884	0.22	3165	0.909	0.912	95.9242	0.221
3.03-3.177	0.248	146	0.226	2776	0.227	3048	0.916	0.916	95.8661	0.231
3.177-3.348	0.265	132	0.226	2514	0.228	2864	0.888	0.912	92.3883	0.233
3.348-3.55	0.249	128	0.227	2436	0.228	2697	0.924	0.92	95.0686	0.233
3.55-3.794	0.252	124	0.213	2358	0.215	2567	0.922	0.935	96.6887	0.221
3.794-4.095	0.223	114	0.183	2163	0.185	2352	0.93	0.942	96.8112	0.197
4.095-4.482	0.181	107	0.164	2023	0.165	2199	0.956	0.952	96.8622	0.187
4.482-5.004	0.216	96	0.169	1825	0.172	1994	0.948	0.957	96.339	0.195
5.004-5.766	0.253	84	0.194	1608	0.197	1741	0.928	0.947	97.1855	0.22
5.766-7.031	0.203	73	0.198	1382	0.199	1497	0.94	0.946	97.1944	0.223
7.031-9.816	0.167	56	0.171	1068	0.171	1146	0.958	0.964	98.0803	0.198
9.816-43.53	0.233	33	0.203	612	0.204	665	0.944	0.952	96.9925	0.23

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