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

ID or keywords:

Entry

Database: PDB / ID: 7veq

Title

Crystal structure of bacterial chemotaxis-dependent pectin-binding protein SPH1118 in an open conformation

Components

SPH1118

Keywords

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

Function / homology

Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Roll / Alpha Beta

Function and homology information

Biological species

Sphingomonas sp. A1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.696 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	7veq.cif.gz	147.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7veq.ent.gz	111.9 KB	Display	PDB format
PDBx/mmJSON format	7veq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7veq_validation.pdf.gz	437.3 KB	Display	wwPDB validaton report
Full document	7veq_full_validation.pdf.gz	439.7 KB	Display
Data in XML	7veq_validation.xml.gz	27 KB	Display
Data in CIF	7veq_validation.cif.gz	40.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ve/7veq ftp://data.pdbj.org/pub/pdb/validation_reports/ve/7veq	HTTPS FTP

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Related structure data

Related structure data	7verC 7vetC 7veuC 7vevSC 7vewC S: Starting model for refinement 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

Deposited unit

A: SPH1118

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	50.855, 151.663, 179.520
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-1136- HOH

#1: Protein	SPH1118 Mass: 68779.172 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphingomonas sp. A1 (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 472 / 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: 2.51 Å³/Da / Density % sol: 51.07 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 2.0 M Ammonium dihydrogenphosphate 0.1 M Tris-HCl 2.0 mM Unsaturated trigalacturonic acid

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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: Oct 24, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.696→48.217 Å / Num. obs: 76813 / % possible obs: 97.8 % / Redundancy: 5.02 % / R_merge(I) obs: 0.086 / Net I/σ(I): 11.1
Reflection shell	Resolution: 1.7→1.74 Å / R_merge(I) obs: 0.555 / Mean I/σ(I) obs: 1.87 / Num. unique obs: 10681

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7VEV

7vev

Resolution: 1.696→48.217 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.95 / Cross valid method: FREE R-VALUE / ESU R: 0.094 / ESU R Free: 0.092
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.195	3841	5 %
R_work	0.1677	72972	-
all	0.169	-	-
obs	-	76813	99.491 %

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: 19.515 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.247 Å²	-0 Å²	0 Å²
2-	-	-0.819 Å²	-0 Å²
3-	-	-	1.066 Å²

Refinement step

Cycle: LAST / Resolution: 1.696→48.217 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4846	0	6	472	5324

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.013	5066
X-RAY DIFFRACTION	r_bond_other_d	0.034	0.017	4793
X-RAY DIFFRACTION	r_angle_refined_deg	1.707	1.647	6893
X-RAY DIFFRACTION	r_angle_other_deg	2.224	1.581	11062
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.267	5	630
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.05	22.829	258
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.632	15	871
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.052	15	29
X-RAY DIFFRACTION	r_chiral_restr	0.099	0.2	644
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	5801
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	1185
X-RAY DIFFRACTION	r_nbd_refined	0.225	0.2	1007
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.218	0.2	4751
X-RAY DIFFRACTION	r_nbtor_refined	0.186	0.2	2564
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.074	0.2	2378
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.13	0.2	320
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.039	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.163	0.2	20
X-RAY DIFFRACTION	r_nbd_other	0.281	0.2	76
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.234	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	2.805	1.825	2490
X-RAY DIFFRACTION	r_mcbond_other	2.785	1.823	2489
X-RAY DIFFRACTION	r_mcangle_it	3.399	2.719	3130
X-RAY DIFFRACTION	r_mcangle_other	3.411	2.72	3131
X-RAY DIFFRACTION	r_scbond_it	4.322	2.105	2575
X-RAY DIFFRACTION	r_scbond_other	4.321	2.106	2576
X-RAY DIFFRACTION	r_scangle_it	5.572	3.002	3763
X-RAY DIFFRACTION	r_scangle_other	5.571	3.003	3764
X-RAY DIFFRACTION	r_lrange_it	5.985	22.156	5889
X-RAY DIFFRACTION	r_lrange_other	5.954	21.855	5798

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
1.696-1.74	0.329	264	0.311	5024	0.312	5632	0.83	0.825	93.892	0.287
1.74-1.788	0.274	272	0.234	5158	0.236	5470	0.886	0.892	99.2687	0.212
1.788-1.84	0.2	267	0.188	5078	0.188	5345	0.937	0.94	100	0.168
1.84-1.896	0.212	261	0.175	4962	0.177	5223	0.934	0.945	100	0.153
1.896-1.959	0.197	253	0.169	4807	0.17	5060	0.945	0.951	100	0.148
1.959-2.027	0.191	245	0.164	4643	0.165	4888	0.95	0.957	100	0.147
2.027-2.104	0.185	234	0.164	4462	0.165	4697	0.954	0.958	99.9787	0.148
2.104-2.189	0.188	228	0.163	4314	0.164	4542	0.956	0.962	100	0.145
2.189-2.286	0.203	219	0.158	4164	0.16	4383	0.951	0.961	100	0.144
2.286-2.398	0.201	209	0.16	3978	0.162	4187	0.949	0.962	100	0.147
2.398-2.527	0.185	198	0.162	3770	0.163	3968	0.955	0.962	100	0.149
2.527-2.68	0.176	190	0.163	3610	0.163	3800	0.962	0.965	100	0.151
2.68-2.864	0.183	177	0.168	3364	0.169	3541	0.962	0.963	100	0.159
2.864-3.093	0.205	166	0.17	3150	0.172	3316	0.945	0.958	100	0.167
3.093-3.387	0.187	154	0.169	2929	0.17	3083	0.955	0.961	100	0.17
3.387-3.784	0.193	139	0.153	2640	0.155	2779	0.957	0.969	100	0.157
3.784-4.365	0.164	124	0.138	2357	0.139	2482	0.968	0.974	99.9597	0.149
4.365-5.335	0.189	107	0.148	2018	0.15	2125	0.968	0.975	100	0.167
5.335-7.499	0.218	84	0.193	1593	0.194	1677	0.953	0.966	100	0.212
7.499-48.217	0.168	50	0.179	950	0.179	1003	0.971	0.971	99.7009	0.215

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