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

ID or keywords:

Entry

Database: PDB / ID: 7veu

Title

Crystal structure of bacterial chemotaxis-dependent pectin-binding protein SPH1118 in complex with galacturonic acid

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 / alpha-D-galactopyranuronic acid

Function and homology information

Biological species

Sphingomonas sp. A1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.736 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	7veu.cif.gz	145.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7veu.ent.gz	109.2 KB	Display	PDB format
PDBx/mmJSON format	7veu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7veu_validation.pdf.gz	834.3 KB	Display	wwPDB validaton report
Full document	7veu_full_validation.pdf.gz	837.5 KB	Display
Data in XML	7veu_validation.xml.gz	25.9 KB	Display
Data in CIF	7veu_validation.cif.gz	38.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ve/7veu ftp://data.pdbj.org/pub/pdb/validation_reports/ve/7veu	HTTPS FTP

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Related structure data

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

70.5 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)	72.686, 86.662, 97.323
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein

SPH1118

Mass: 70050.602 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.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃

#3: Sugar

ChemComp-ADA / alpha-D-galactopyranuronic acid / alpha-D-galacturonic acid / D-galacturonic acid / galacturonic acid / ALPHA D-GALACTURONIC ACID

Type: D-saccharide, alpha linking / Mass: 194.139 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₀O₇ / Feature type: SUBJECT OF INVESTIGATION

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 345 / 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: 2.19 Å³/Da / Density % sol: 43.78 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 40% PEG600 0.1 M Citrate 50 mM Galacturonic 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: Feb 14, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.736→42.4 Å / Num. obs: 63700 / % possible obs: 99.3 % / Redundancy: 6.17 % / R_merge(I) obs: 0.068 / Net I/σ(I): 25.6
Reflection shell	Resolution: 1.74→1.84 Å / R_merge(I) obs: 0.529 / Num. unique obs: 10044

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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: 1.736→40.436 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.957 / Cross valid method: FREE R-VALUE / ESU R: 0.101 / ESU R Free: 0.095
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1812	3185	5 %
R_work	0.1557	60515	-
all	0.157	-	-
obs	-	63700	99.257 %

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: 18.611 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.877 Å²	0 Å²	-0 Å²
2-	-	-1.128 Å²	0 Å²
3-	-	-	0.251 Å²

Refinement step

Cycle: LAST / Resolution: 1.736→40.436 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4872	0	31	345	5248

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.013	5096
X-RAY DIFFRACTION	r_bond_other_d	0.034	0.017	4813
X-RAY DIFFRACTION	r_angle_refined_deg	1.72	1.65	6931
X-RAY DIFFRACTION	r_angle_other_deg	2.223	1.584	11107
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.325	5	629
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.914	22.759	261
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.777	15	869
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.052	15	30
X-RAY DIFFRACTION	r_chiral_restr	0.097	0.2	650
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	5808
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	1188
X-RAY DIFFRACTION	r_nbd_refined	0.225	0.2	1012
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.217	0.2	4655
X-RAY DIFFRACTION	r_nbtor_refined	0.185	0.2	2578
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.075	0.2	2378
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.135	0.2	257
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.087	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.164	0.2	14
X-RAY DIFFRACTION	r_nbd_other	0.274	0.2	73
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.146	0.2	19
X-RAY DIFFRACTION	r_mcbond_it	2.456	1.727	2492
X-RAY DIFFRACTION	r_mcbond_other	2.452	1.727	2491
X-RAY DIFFRACTION	r_mcangle_it	3.02	2.571	3129
X-RAY DIFFRACTION	r_mcangle_other	3.021	2.572	3130
X-RAY DIFFRACTION	r_scbond_it	4.281	2.032	2604
X-RAY DIFFRACTION	r_scbond_other	4.28	2.032	2604
X-RAY DIFFRACTION	r_scangle_it	5.645	2.888	3802
X-RAY DIFFRACTION	r_scangle_other	5.645	2.889	3803
X-RAY DIFFRACTION	r_lrange_it	5.827	20.831	5834
X-RAY DIFFRACTION	r_lrange_other	5.813	20.654	5778

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
1.736-1.781	0.257	227	0.226	4314	0.228	4661	0.903	0.911	97.4254	0.198
1.781-1.829	0.218	225	0.18	4274	0.182	4556	0.939	0.944	98.7489	0.152
1.829-1.882	0.21	219	0.164	4168	0.166	4450	0.94	0.953	98.5843	0.136
1.882-1.94	0.204	214	0.156	4074	0.158	4328	0.95	0.957	99.0758	0.129
1.94-2.004	0.177	207	0.144	3928	0.146	4172	0.959	0.966	99.1131	0.12
2.004-2.074	0.188	201	0.138	3819	0.141	4060	0.956	0.968	99.0148	0.116
2.074-2.152	0.17	194	0.142	3676	0.143	3892	0.964	0.97	99.4347	0.121
2.152-2.239	0.168	188	0.14	3573	0.141	3791	0.966	0.972	99.2087	0.122
2.239-2.339	0.194	181	0.141	3445	0.144	3642	0.953	0.966	99.5607	0.125
2.339-2.452	0.164	172	0.143	3268	0.144	3451	0.97	0.972	99.6813	0.127
2.452-2.585	0.141	165	0.142	3145	0.142	3319	0.976	0.976	99.7288	0.128
2.585-2.741	0.183	156	0.151	2963	0.152	3125	0.963	0.97	99.808	0.138
2.741-2.929	0.169	149	0.157	2825	0.158	2978	0.968	0.97	99.8657	0.146
2.929-3.162	0.187	138	0.157	2623	0.158	2767	0.961	0.968	99.7832	0.15
3.162-3.462	0.194	129	0.158	2439	0.16	2568	0.96	0.969	100	0.157
3.462-3.867	0.173	115	0.151	2193	0.152	2308	0.966	0.971	100	0.156
3.867-4.458	0.142	103	0.134	1962	0.134	2065	0.975	0.975	100	0.145
4.458-5.444	0.174	89	0.163	1693	0.164	1782	0.973	0.973	100	0.177
5.444-7.63	0.208	70	0.217	1329	0.216	1399	0.962	0.959	100	0.225
7.63-40.436	0.246	43	0.207	804	0.209	856	0.953	0.969	98.9486	0.236

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