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

ID or keywords:

Entry

Database: PDB / ID: 9eqq

Title

Uhgb_MS mannoside synthase from an unknown human gut bacterium in complex with Mannose

Components

Uhgb_MS mannoside synthase from an unknown human gut bacterium

Keywords

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

Function / homology

alpha-D-mannopyranose

Function and homology information

Biological species

metagenome (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.55 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	9eqq.cif.gz	89.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9eqq.ent.gz	64.1 KB	Display	PDB format
PDBx/mmJSON format	9eqq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9eqq_validation.pdf.gz	830.2 KB	Display	wwPDB validaton report
Full document	9eqq_full_validation.pdf.gz	830.8 KB	Display
Data in XML	9eqq_validation.xml.gz	18.3 KB	Display
Data in CIF	9eqq_validation.cif.gz	25.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/eq/9eqq ftp://data.pdbj.org/pub/pdb/validation_reports/eq/9eqq	HTTPS FTP

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Related structure data

Related structure data	9ergC 9erhC 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
Related items in Molecule of the Month	#247 - Jul 2020 Myelin-associated Glycoprotein similarity (1) #74 - Feb 2006 alpha-Amylase similarity (1) #83 - Nov 2006 Fibrin similarity (1)

Deposited unit

A: Uhgb_MS mannoside synthase from an unknown human gut bacterium

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	176.629, 176.629, 83.539
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	178
Space group name H-M	P6₁22

Components on special symmetry positions

ID	Model	Components
1	1	A-575- HOH
2	1	A-584- HOH
3	1	A-648- HOH
4	1	A-656- HOH
5	1	A-660- HOH

#1: Protein

Uhgb_MS mannoside synthase from an unknown human gut bacterium

Mass: 39182.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host:

Escherichia coli (E. coli)

#2: Sugar

ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose

Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₂O₆ / Feature type: SUBJECT OF INVESTIGATION

#3: Chemical

ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL

Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 160 / 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: 4.8 Å³/Da / Density % sol: 74.38 %
Crystal grow	Temperature: 285 K / Method: vapor diffusion, sitting drop Details: 0.2 M Calcium acetate, 0.1 M Imidazole pH 8.0, 20 %PEG 1000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 10, 2021
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.978565 Å / Relative weight: 1
Reflection	Resolution: 2.55→47.586 Å / Num. obs: 1030781 / % possible obs: 100 % / Redundancy: 40.3 % / R_merge(I) obs: 0.102 / Net I/σ(I): 4.8
Reflection shell	Resolution: 2.55→2.69 Å / R_merge(I) obs: 0.718 / Num. unique obs: 3653

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.55→47.586 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.949 / SU B: 5.796 / SU ML: 0.126 / Cross valid method: FREE R-VALUE / ESU R: 0.224 / ESU R Free: 0.186
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2067	1278	5.007 %
R_work	0.1795	24246	-
all	0.181	-	-
obs	-	25524	99.969 %

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: 59.848 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.041 Å²	0.021 Å²	0 Å²
2-	-	0.041 Å²	0 Å²
3-	-	-	-0.134 Å²

Refinement step

Cycle: LAST / Resolution: 2.55→47.586 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2733	0	16	160	2909

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.012	2820
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2587
X-RAY DIFFRACTION	r_angle_refined_deg	1.392	1.822	3825
X-RAY DIFFRACTION	r_angle_other_deg	0.48	1.755	5989
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.675	5	346
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.089	5	12
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.441	10	460
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.744	10	131
X-RAY DIFFRACTION	r_chiral_restr	0.064	0.2	411
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	3293
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	631
X-RAY DIFFRACTION	r_nbd_refined	0.185	0.2	462
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.191	0.2	2370
X-RAY DIFFRACTION	r_nbtor_refined	0.176	0.2	1321
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	1457
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.154	0.2	141
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.032	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.084	0.2	6
X-RAY DIFFRACTION	r_nbd_other	0.131	0.2	70
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.124	0.2	24
X-RAY DIFFRACTION	r_mcbond_it	4.54	6.143	1387
X-RAY DIFFRACTION	r_mcbond_other	4.537	6.143	1387
X-RAY DIFFRACTION	r_mcangle_it	6.45	11.028	1732
X-RAY DIFFRACTION	r_mcangle_other	6.449	11.03	1733
X-RAY DIFFRACTION	r_scbond_it	4.936	6.569	1433
X-RAY DIFFRACTION	r_scbond_other	4.934	6.568	1434
X-RAY DIFFRACTION	r_scangle_it	7.558	11.88	2093
X-RAY DIFFRACTION	r_scangle_other	7.556	11.879	2094
X-RAY DIFFRACTION	r_lrange_it	9.56	56.27	2998
X-RAY DIFFRACTION	r_lrange_other	9.575	56.238	2971

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

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	WR_factor R_work
2.55-2.616	0.311	85	0.26	1762	0.263	1847	0.954	0.969	0.227
2.616-2.688	0.33	95	0.246	1704	0.25	1799	0.947	0.974	0.213
2.688-2.765	0.274	89	0.223	1669	0.226	1758	0.959	0.975	0.193
2.765-2.85	0.269	85	0.214	1608	0.217	1693	0.959	0.975	0.185
2.85-2.943	0.242	95	0.197	1551	0.199	1646	0.965	0.977	0.172
2.943-3.046	0.269	78	0.206	1538	0.209	1616	0.959	0.973	0.185
3.046-3.16	0.231	87	0.207	1460	0.208	1547	0.967	0.973	0.191
3.16-3.289	0.233	77	0.216	1402	0.217	1479	0.97	0.972	0.203
3.289-3.434	0.242	82	0.21	1362	0.212	1444	0.966	0.974	0.202
3.434-3.601	0.273	72	0.222	1314	0.225	1386	0.952	0.972	0.216
3.601-3.795	0.199	49	0.189	1261	0.189	1310	0.975	0.981	0.186
3.795-4.023	0.164	70	0.168	1174	0.168	1244	0.985	0.986	0.17
4.023-4.299	0.162	44	0.147	1134	0.148	1178	0.982	0.988	0.153
4.299-4.64	0.147	61	0.133	1050	0.134	1111	0.987	0.99	0.144
4.64-5.078	0.185	32	0.128	975	0.13	1007	0.983	0.99	0.139
5.078-5.67	0.176	50	0.146	895	0.147	945	0.981	0.988	0.161
5.67-6.531	0.17	42	0.138	797	0.14	839	0.984	0.989	0.15
6.531-7.962	0.155	30	0.157	685	0.157	715	0.984	0.985	0.171
7.962-11.105	0.204	34	0.162	551	0.164	585	0.975	0.985	0.187
11.105-47.586	0.228	21	0.276	354	0.273	375	0.978	0.938	0.299

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