PDB-8ip2: Escherichia coli OpgG mutant-D361N with beta-1,2-glucan

ID or keywords:

Entry

Database: PDB / ID: 8ip2

Title

Escherichia coli OpgG mutant-D361N with beta-1,2-glucan

Components

Glucans biosynthesis protein G

Keywords

HYDROLASE / Beta-1 / 2-glucanase

Function / homology

Function and homology information

beta-glucan biosynthetic process / catalytic activity / outer membrane-bounded periplasmic space / carbohydrate binding
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.81 Å

Authors

Motouchi, S. / Nakajima, M.

Funding support

Japan, 1items

Citation

Journal: Commun Biol / Year: 2023
Title: Identification of enzymatic functions of osmo-regulated periplasmic glucan biosynthesis proteins from Escherichia coli reveals a novel glycoside hydrolase family.
Authors: Motouchi, S. / Kobayashi, K. / Nakai, H. / Nakajima, M.

History

Deposition	Mar 13, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 13, 2024	Provider: repository / Type: Initial release
Revision 1.1	Jul 10, 2024	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2	Jul 17, 2024	Group: Database references / Category: citation Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8ip2.cif.gz	200.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8ip2.ent.gz	155.6 KB	Display	PDB format
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Validation report

Summary document	8ip2_validation.pdf.gz	727 KB	Display	wwPDB validaton report
Full document	8ip2_full_validation.pdf.gz	729.4 KB	Display
Data in XML	8ip2_validation.xml.gz	20.1 KB	Display
Data in CIF	8ip2_validation.cif.gz	28.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ip/8ip2 ftp://data.pdbj.org/pub/pdb/validation_reports/ip/8ip2	HTTPS FTP

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Related structure data

Related structure data	8ioxC 8ip1C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#198 - Jun 2016 Beta-galactosidase similarity (2) #39 - Mar 2003 lac Repressor similarity (2) #203 - Nov 2016 Aminopeptidase 1 and Autophagy similarity (1)

Deposited unit

A: Glucans biosynthesis protein G

hetero molecules

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

1

A: Glucans biosynthesis protein G

hetero molecules

A: Glucans biosynthesis protein G

hetero molecules

defined by author&software
123 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	62.821, 80.970, 213.225
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-625- HOH
2	1	A-719- HOH

#1: Protein

Glucans biosynthesis protein G

Mass: 59052.453 Da / Num. of mol.: 1 / Mutation: D361N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: opgG / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P33136

#2: Polysaccharide

beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D- ...

Type: oligosaccharide / Mass: 2612.268 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,16,15/[a2122h-1b_1-5]/1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1/a2-b1_b2-c1_c2-d1_d2-e1_e2-f1_f2-g1_g2-h1_h2-i1_i2-j1_j2-k1_k2-l1_l2-m1_m2-n1_n2-o1_o2-p1	WURCS	PDB2Glycan 1.1.0
[][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{}}}}}}}}}}}}}}}}	LINUCS	PDB-CARE

#3: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.3 Å³/Da / Density % sol: 46.42 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: MMT (pH 5.0), PEG400

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 4, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.81→48.34 Å / Num. obs: 50021 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC_1/2: 0.999 / Net I/σ(I): 17.2
Reflection shell	Resolution: 1.81→1.85 Å / Num. unique obs: 2971 / CC_1/2: 0.891

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.81→48.34 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.941 / Cross valid method: FREE R-VALUE / ESU R: 0.248 / ESU R Free: 0.138
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.254	2535	5.074 %
R_work	0.2134	47424	-
all	0.215	-	-
obs	-	49959	99.876 %

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: 41.948 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.123 Å²	-0 Å²	0 Å²
2-	-	-0.075 Å²	-0 Å²
3-	-	-	0.198 Å²

Refinement step

Cycle: LAST / Resolution: 1.81→48.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3819	0	177	122	4118

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.013	4111
X-RAY DIFFRACTION	r_bond_other_d	0.034	0.015	3825
X-RAY DIFFRACTION	r_angle_refined_deg	1.719	1.723	5605
X-RAY DIFFRACTION	r_angle_other_deg	3.379	1.646	8806
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.457	5	475
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.452	22.477	214
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.08	15	650
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.251	15	25
X-RAY DIFFRACTION	r_chiral_restr	0.098	0.2	576
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	4453
X-RAY DIFFRACTION	r_gen_planes_other	0.016	0.02	933
X-RAY DIFFRACTION	r_nbd_refined	0.201	0.2	632
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.23	0.2	3618
X-RAY DIFFRACTION	r_nbtor_refined	0.177	0.2	1952
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.115	0.2	2034
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.148	0.2	187
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.025	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.142	0.2	9
X-RAY DIFFRACTION	r_nbd_other	0.239	0.2	69
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.146	0.2	11
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.002	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	0.28	4.352	1909
X-RAY DIFFRACTION	r_mcbond_other	0.294	4.35	1908
X-RAY DIFFRACTION	r_mcangle_it	0.491	6.511	2381
X-RAY DIFFRACTION	r_mcangle_other	0.498	6.514	2382
X-RAY DIFFRACTION	r_scbond_it	0.286	4.519	2202
X-RAY DIFFRACTION	r_scbond_other	0.286	4.52	2203
X-RAY DIFFRACTION	r_scangle_it	0.482	6.653	3224
X-RAY DIFFRACTION	r_scangle_other	0.482	6.654	3225
X-RAY DIFFRACTION	r_lrange_it	0.721	48.541	4277
X-RAY DIFFRACTION	r_lrange_other	0.723	64.639	4261
X-RAY DIFFRACTION	r_rigid_bond_restr	13.057	3	7862

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.81-1.857	0.35	196	0.369	3435	X-RAY DIFFRACTION	99.9449
1.857-1.908	0.389	155	0.344	3450	X-RAY DIFFRACTION	99.9723
1.908-1.963	0.358	181	0.312	3277	X-RAY DIFFRACTION	100
1.963-2.023	0.3	167	0.296	3175	X-RAY DIFFRACTION	99.7612
2.023-2.09	0.295	181	0.276	3075	X-RAY DIFFRACTION	99.9079
2.09-2.163	0.316	171	0.252	2973	X-RAY DIFFRACTION	99.8729
2.163-2.244	0.325	155	0.247	2925	X-RAY DIFFRACTION	99.9027
2.244-2.336	0.329	149	0.243	2793	X-RAY DIFFRACTION	99.9321
2.336-2.439	0.269	124	0.211	2709	X-RAY DIFFRACTION	99.8942
2.439-2.558	0.27	118	0.221	2570	X-RAY DIFFRACTION	100
2.558-2.696	0.236	136	0.216	2460	X-RAY DIFFRACTION	99.923
2.696-2.859	0.256	109	0.208	2327	X-RAY DIFFRACTION	99.918
2.859-3.055	0.264	114	0.223	2172	X-RAY DIFFRACTION	99.9126
3.055-3.299	0.281	113	0.217	2030	X-RAY DIFFRACTION	99.8602
3.299-3.612	0.216	98	0.202	1883	X-RAY DIFFRACTION	99.6479
3.612-4.036	0.227	115	0.179	1695	X-RAY DIFFRACTION	99.6696
4.036-4.655	0.206	66	0.152	1555	X-RAY DIFFRACTION	99.6312
4.655-5.688	0.204	65	0.166	1312	X-RAY DIFFRACTION	99.855
5.688-7.989	0.226	76	0.186	998	X-RAY DIFFRACTION	100
7.989-48.34	0.209	46	0.19	610	X-RAY DIFFRACTION	99.5448

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