PDB-7oms: Bs164 in complex with mannocyclophellitol aziridine

ID or keywords:

Entry

Database: PDB / ID: 7oms

Title

Bs164 in complex with mannocyclophellitol aziridine

Components

Glyco_hydro_42M domain-containing protein

Keywords

HYDROLASE / Inhibitor complex

Function / homology

Glycoside hydrolase, family 42 / Beta-galactosidase trimerisation / Beta-galactosidase trimerisation domain / beta-galactosidase activity / Class I glutamine amidotransferase-like / Glycoside hydrolase superfamily / carbohydrate metabolic process / Chem-VKH / Beta-galactosidase trimerisation domain-containing protein

Function and homology information

Biological species

Bacteroides salyersiae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.05 Å

Authors

McGregor, N. / Beenakker, T. / Kuo, C.L. / Wong, C.S. / Offren, W.A. / Armstrong, Z. / Codee, J.D.C. / Aerts, J.M.F.G. / Florea, B.I. / Overkleeft, H. / Davies, G.J.

Citation

Journal: Org.Biomol.Chem. / Year: 2022
Title: Synthesis of broad-specificity activity-based probes for exo -beta-mannosidases.
Authors: McGregor, N.G.S. / Kuo, C.L. / Beenakker, T.J.M. / Wong, C.S. / Offen, W.A. / Armstrong, Z. / Florea, B.I. / Codee, J.D.C. / Overkleeft, H.S. / Aerts, J.M.F.G. / Davies, G.J.

History

Deposition	May 24, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 2, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.2	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7oms.cif.gz	1.5 MB	Display	PDBx/mmCIF format
PDB format	pdb7oms.ent.gz		Display	PDB format
PDBx/mmJSON format	7oms.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/om/7oms ftp://data.pdbj.org/pub/pdb/validation_reports/om/7oms	HTTPS FTP

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Related structure data

Related structure data	7odjC 7omiC 7op6C 7op7C 6t7gS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7oms-2 7omi-2 7omi-1 4oif-d 3tts-1 5dfa-d 4ojy-d 3tty-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

AAA: Glyco_hydro_42M domain-containing protein

DDD: Glyco_hydro_42M domain-containing protein

CCC: Glyco_hydro_42M domain-containing protein

BBB: Glyco_hydro_42M domain-containing protein

FFF: Glyco_hydro_42M domain-containing protein

EEE: Glyco_hydro_42M domain-containing protein

hetero molecules

462 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

AAA: Glyco_hydro_42M domain-containing protein

CCC: Glyco_hydro_42M domain-containing protein

BBB: Glyco_hydro_42M domain-containing protein

hetero molecules

defined by author&software
Evidence: gel filtration
231 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

DDD: Glyco_hydro_42M domain-containing protein

FFF: Glyco_hydro_42M domain-containing protein

EEE: Glyco_hydro_42M domain-containing protein

hetero molecules

defined by author&software
231 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	69.335, 103.959, 170.127
Angle α, β, γ (deg.)	92.272, 97.708, 106.397
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	Chains AAA DDD
2	1	Chains AAA CCC
3	1	Chains AAA BBB
4	1	Chains AAA FFF
5	1	Chains AAA EEE
6	1	Chains DDD CCC
7	1	Chains DDD BBB
8	1	Chains DDD FFF
9	1	Chains DDD EEE
10	1	Chains CCC BBB
11	1	Chains CCC FFF
12	1	Chains CCC EEE
13	1	Chains BBB FFF
14	1	Chains BBB EEE
15	1	Chains FFF EEE

#1: Protein	Glyco_hydro_42M domain-containing protein Mass: 76676.672 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides salyersiae (bacteria) / Gene: HMPREF1071_03408 / Production host: Escherichia coli (E. coli) / References: UniProt: I9SUA3
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-VKH / (1~{R},2~{R},3~{S},4~{R},5~{R},6~{R})-5-(hydroxymethyl)-7-azabicyclo[4.1.0]heptane-2,3,4-triol Mass: 178.206 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₇H₁₆NO₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 795 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	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: 2.53 Å³/Da / Density % sol: 51.3 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M ammonium tartrate pH 7.0, 13 % PEG 3350

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Data collection

Diffraction	Mean temperature: 293 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.976246 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 24, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.976246 Å / Relative weight: 1
Reflection	Resolution: 2.05→99.597 Å / Num. obs: 277094 / % possible obs: 98.1 % / Redundancy: 3.5 % / CC_1/2: 0.98 / Net I/σ(I): 3.2
Reflection shell	Resolution: 2.05→2.09 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 13602 / CC_1/2: 0.655

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
DIALS		data reduction
xia2		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6T7G

6t7g

Resolution: 2.05→99.4 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.929 / SU B: 8.692 / SU ML: 0.213 / Cross valid method: FREE R-VALUE / ESU R: 0.23 / ESU R Free: 0.19
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2583	13624	4.929 %
R_work	0.2231	262789	-
all	0.225	-	-
obs	-	276413	97.814 %

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: 46.039 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.451 Å²	2.825 Å²	-2.623 Å²
2-	-	3.296 Å²	-0.177 Å²
3-	-	-	-5.76 Å²

Refinement step

Cycle: LAST / Resolution: 2.05→99.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	31275	0	134	795	32204

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	32260
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	28884
X-RAY DIFFRACTION	r_angle_refined_deg	1.437	1.64	43706
X-RAY DIFFRACTION	r_angle_other_deg	1.287	1.575	67232
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.648	5	3903
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.282	23.928	1609
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.5	15	5351
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.399	15	88
X-RAY DIFFRACTION	r_chiral_restr	0.067	0.2	4186
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	35950
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	6926
X-RAY DIFFRACTION	r_nbd_refined	0.198	0.2	6334
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.179	0.2	27512
X-RAY DIFFRACTION	r_nbtor_refined	0.171	0.2	15608
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.076	0.2	14287
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.16	0.2	1201
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.057	0.2	8
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.185	0.2	20
X-RAY DIFFRACTION	r_nbd_other	0.277	0.2	75
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.296	0.2	5
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.114	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	4.216	4.823	15639
X-RAY DIFFRACTION	r_mcbond_other	4.217	4.823	15638
X-RAY DIFFRACTION	r_mcangle_it	5.703	7.228	19533
X-RAY DIFFRACTION	r_mcangle_other	5.703	7.228	19534
X-RAY DIFFRACTION	r_scbond_it	4.341	5.12	16621
X-RAY DIFFRACTION	r_scbond_other	4.341	5.12	16622
X-RAY DIFFRACTION	r_scangle_it	6.222	7.54	24173
X-RAY DIFFRACTION	r_scangle_other	6.222	7.54	24174
X-RAY DIFFRACTION	r_lrange_it	7.784	54.893	36282
X-RAY DIFFRACTION	r_lrange_other	7.785	54.874	36190
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.061	0.05	22413
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.06	0.05	22301
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.06	0.05	22389
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.065	0.05	22326
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.064	0.05	22323
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.059	0.05	22403
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.059	0.05	22435
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.061	0.05	22401
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.061	0.05	22480
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.061	0.05	22475
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.06	0.05	22500
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.063	0.05	22530
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.065	0.05	22430
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.062	0.05	22515
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.064	0.05	22473

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 (%)
2.05-2.103	0.383	945	0.374	19302	X-RAY DIFFRACTION	96.373
2.103-2.161	0.348	1037	0.343	18592	X-RAY DIFFRACTION	96.4475
2.161-2.223	0.328	934	0.316	18256	X-RAY DIFFRACTION	97.0025
2.223-2.292	0.344	922	0.314	17657	X-RAY DIFFRACTION	96.8615
2.292-2.367	0.307	862	0.273	17291	X-RAY DIFFRACTION	97.3873
2.367-2.45	0.299	866	0.258	16719	X-RAY DIFFRACTION	97.494
2.45-2.543	0.286	844	0.24	16230	X-RAY DIFFRACTION	97.7221
2.543-2.646	0.283	800	0.232	15588	X-RAY DIFFRACTION	97.8739
2.646-2.764	0.267	797	0.224	14884	X-RAY DIFFRACTION	97.6401
2.764-2.899	0.252	772	0.211	14297	X-RAY DIFFRACTION	98.0863
2.899-3.056	0.261	698	0.208	13644	X-RAY DIFFRACTION	98.3137
3.056-3.241	0.255	684	0.207	12923	X-RAY DIFFRACTION	98.5729
3.241-3.465	0.24	630	0.207	12242	X-RAY DIFFRACTION	98.7798
3.465-3.742	0.249	571	0.21	11259	X-RAY DIFFRACTION	98.7809
3.742-4.099	0.223	562	0.19	10501	X-RAY DIFFRACTION	99.1131
4.099-4.582	0.213	485	0.177	9429	X-RAY DIFFRACTION	99.14
4.582-5.291	0.216	427	0.185	8423	X-RAY DIFFRACTION	99.282
5.291-6.478	0.241	341	0.213	7083	X-RAY DIFFRACTION	99.5041
6.478-9.155	0.228	286	0.205	5454	X-RAY DIFFRACTION	99.6874
9.155-99.4	0.266	161	0.225	3015	X-RAY DIFFRACTION	99.4987

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