PDB-9erh: Uhgb_MS mannoside synthase from an unknown human gut bacterium in...

ID or keywords:

Entry

Database: PDB / ID: 9erh

Title

Uhgb_MS mannoside synthase from an unknown human gut bacterium in complex with 1,2-beta-mannobiose

Components

Uhgb_MS mannoside synthase from an unknown human gut bacterium in complex with 1,2-beta-mannobiose

Keywords

CARBOHYDRATE / Carbohydrate methabolism / Carbohydrate assimilation / carbohydrate processing / Inflammatory bowel bisease

Biological species

metagenome (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.65 Å

Authors

Cioci, G. / Ladeveze, S. / Potocki-Veronese, G.

Funding support

1items

Citation

Journal: To Be Published
Title: Structure-function studies of novel bacterial mannoside synthase
Authors: Cioci, G. / Ladeveze, S.

History

Deposition	Mar 22, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 8, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9erh.cif.gz	152.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9erh.ent.gz	115.8 KB	Display	PDB format
PDBx/mmJSON format	9erh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9erh_validation.pdf.gz	1.9 MB	Display	wwPDB validaton report
Full document	9erh_full_validation.pdf.gz	1.9 MB	Display
Data in XML	9erh_validation.xml.gz	28 KB	Display
Data in CIF	9erh_validation.cif.gz	36.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/er/9erh ftp://data.pdbj.org/pub/pdb/validation_reports/er/9erh	HTTPS FTP

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Related structure data

Related structure data	9eqqC 9ergC C: citing same article (ref.)

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Uhgb_MS mannoside synthase from an unknown human gut bacterium in complex with 1,2-beta-mannobiose

B: Uhgb_MS mannoside synthase from an unknown human gut bacterium in complex with 1,2-beta-mannobiose

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration, dimer

Unit cell

Length a, b, c (Å)	178.183, 178.183, 83.675
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	169
Space group name H-M	P6₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ASN / End label comp-ID: ASN / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 347 / Label seq-ID: 1 - 347

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

#1: Protein

Uhgb_MS mannoside synthase from an unknown human gut bacterium in complex with 1,2-beta-mannobiose

Mass: 40253.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host:

Escherichia coli (E. coli)

#2: Polysaccharide

beta-D-mannopyranose-(1-2)-alpha-D-mannopyranose

Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source

#3: Chemical

ChemComp-SO4 / SULFATE ION

Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄ / Feature type: SUBJECT OF INVESTIGATION

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

Y

Has protein modification

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: 4.76 Å³/Da / Density % sol: 74.18 %
Crystal grow	Temperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ALBA

/ Beamline: XALOC / Wavelength: 0.97926 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 17, 2023

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97926 Å / Relative weight: 1

Reflection twin

Type	Crystal-ID	ID	Operator	Domain-ID	Fraction
pseudo-merohedral	1	1	H, K, L	1	0.5438
pseudo-merohedral	2	2	-K, -H, -L	2	0.4562

Reflection

Resolution: 2.65→154.31 Å / Num. obs: 44200 / % possible obs: 100 % / Redundancy: 5.7 % / R_merge(I) obs: 0.076 / Net I/σ(I): 7.1

Reflection shell

Resolution: 2.65→2.79 Å / R_merge(I) obs: 0.752 / Num. unique obs: 6415

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.65→50 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.943 / SU B: 5.375 / SU ML: 0.116 / Cross valid method: FREE R-VALUE / ESU R: 0.051 / ESU R Free: 0.038
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1816	2184	4.944 %
R_work	0.1689	41990	-
all	0.17	-	-
obs	-	44174	99.937 %

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: 71.379 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.916 Å²	-0 Å²	-0 Å²
2-	-	-3.916 Å²	-0 Å²
3-	-	-	7.833 Å²

Refinement step

Cycle: LAST / Resolution: 2.65→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5466	0	56	11	5533

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.002	0.012	5666
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	5192
X-RAY DIFFRACTION	r_angle_refined_deg	0.732	1.822	7692
X-RAY DIFFRACTION	r_angle_other_deg	0.289	1.756	12030
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.833	5	692
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	1.87	5	24
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.006	10	924
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	8.43	10	260
X-RAY DIFFRACTION	r_chiral_restr	0.032	0.2	834
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	6584
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1264
X-RAY DIFFRACTION	r_nbd_refined	0.148	0.2	844
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.177	0.2	4761
X-RAY DIFFRACTION	r_nbtor_refined	0.17	0.2	2633
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	2705
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.09	0.2	82
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.18	0.2	3
X-RAY DIFFRACTION	r_nbd_other	0.128	0.2	24
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.05	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	1.898	7.143	2774
X-RAY DIFFRACTION	r_mcbond_other	1.898	7.143	2774
X-RAY DIFFRACTION	r_mcangle_it	3.312	12.843	3464
X-RAY DIFFRACTION	r_mcangle_other	3.311	12.844	3465
X-RAY DIFFRACTION	r_scbond_it	1.679	7.326	2892
X-RAY DIFFRACTION	r_scbond_other	1.679	7.325	2893
X-RAY DIFFRACTION	r_scangle_it	3.007	13.399	4228
X-RAY DIFFRACTION	r_scangle_other	3.007	13.398	4229
X-RAY DIFFRACTION	r_lrange_it	5.095	65.169	5693
X-RAY DIFFRACTION	r_lrange_other	5.095	65.166	5694
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.037	0.05	11043

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.03703	0.05011
1	2	A	X-RAY DIFFRACTION	Local ncs	0.03703	0.05011

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 (%)
2.65-2.719	0.451	162	0.39	3082	X-RAY DIFFRACTION	99.5092
2.719-2.793	0.425	139	0.339	3033	X-RAY DIFFRACTION	100
2.793-2.874	0.293	161	0.259	2931	X-RAY DIFFRACTION	100
2.874-2.963	0.218	155	0.207	2817	X-RAY DIFFRACTION	100
2.963-3.06	0.206	136	0.214	2751	X-RAY DIFFRACTION	100
3.06-3.167	0.245	137	0.192	2680	X-RAY DIFFRACTION	100
3.167-3.287	0.207	171	0.189	2520	X-RAY DIFFRACTION	100
3.287-3.421	0.204	108	0.185	2520	X-RAY DIFFRACTION	100
3.421-3.573	0.147	111	0.172	2396	X-RAY DIFFRACTION	99.9601
3.573-3.747	0.188	109	0.172	2272	X-RAY DIFFRACTION	100
3.747-3.949	0.174	132	0.164	2176	X-RAY DIFFRACTION	100
3.949-4.189	0.151	105	0.153	2056	X-RAY DIFFRACTION	100
4.189-4.478	0.174	79	0.132	1939	X-RAY DIFFRACTION	99.901
4.478-4.836	0.109	86	0.118	1804	X-RAY DIFFRACTION	99.8415
4.836-5.297	0.104	88	0.117	1663	X-RAY DIFFRACTION	99.8859
5.297-5.922	0.121	83	0.147	1505	X-RAY DIFFRACTION	100
5.922-6.836	0.14	64	0.147	1347	X-RAY DIFFRACTION	99.9292
6.836-8.369	0.171	74	0.159	1111	X-RAY DIFFRACTION	100
8.369-11.818	0.179	55	0.14	884	X-RAY DIFFRACTION	99.8936
11.818-50	0.329	29	0.264	503	X-RAY DIFFRACTION	99.6255

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