PDB-6t6g: Bacteroides salyersiae GH164 beta-mannosidase in complex with noe...

ID or keywords:

Entry

Database: PDB / ID: 6t6g

Title

Bacteroides salyersiae GH164 beta-mannosidase in complex with noeuromycin

Components

Glyco_hydro_42M domain-containing protein

Keywords

HYDROLASE / Beta-mannosidase Glycoside Hydrolase

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-MNM / Beta-galactosidase trimerisation domain-containing protein

Function and homology information

Biological species

Bacteroides salyersiae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.06 Å

Authors

Armstrong, Z. / Davies, G.

Funding support

United Kingdom, 2items

Citation

Journal: J.Biol.Chem. / Year: 2020
Title: Structure and function ofBs164 beta-mannosidase fromBacteroides salyersiaethe founding member of glycoside hydrolase family GH164.
Authors: Armstrong, Z. / Davies, G.J.

History

Deposition	Oct 18, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 1, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jan 8, 2020	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2	Apr 8, 2020	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3	Jan 24, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6t6g.cif.gz	2.6 MB	Display	PDBx/mmCIF format
PDB format	pdb6t6g.ent.gz		Display	PDB format
PDBx/mmJSON format	6t6g.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6t6g_validation.pdf.gz	2.3 MB	Display	wwPDB validaton report
Full document	6t6g_full_validation.pdf.gz	2.3 MB	Display
Data in XML	6t6g_validation.xml.gz	136.6 KB	Display
Data in CIF	6t6g_validation.cif.gz	191.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t6/6t6g ftp://data.pdbj.org/pub/pdb/validation_reports/t6/6t6g	HTTPS FTP

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Related structure data

Related structure data	6t5oSC 6t75C 6t7gC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6t6g-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: assay for oligomerization
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)	69.754, 105.096, 170.544
Angle α, β, γ (deg.)	92.602, 97.209, 105.096
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	Chains A D
2	1	Chains A C
3	1	Chains A B
4	1	Chains A F
5	1	Chains A E
6	2	Chains D C
7	2	Chains D B
8	2	Chains D F
9	2	Chains D E
10	2	Chains C B
11	2	Chains C F
12	2	Chains C E
13	3	Chains B F
14	3	Chains B E
15	3	Chains F E

NCS ensembles :

ID
1
2
3

#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.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-MNM / (2S,3S,4R,5R)-2,3,4-TRIHYDROXY-5-HYDROXYMETHYL-PIPERIDINE Mass: 163.172 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄ / 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.: 1029 / 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: 2.59 Å³/Da / Density % sol: 52.59 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M ammonium tartrate pH 7.0, 13 % PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.916 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: 0.916 Å / Relative weight: 1
Reflection	Resolution: 2.06→101.13 Å / Num. obs: 280992 / % possible obs: 98.3 % / Redundancy: 3.5 % / CC_1/2: 0.986 / Net I/σ(I): 5.2
Reflection shell	Resolution: 2.06→2.1 Å / Num. unique obs: 13781 / CC_1/2: 0.6

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0257	refinement
DIALS		data reduction
xia2		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6T5O

6t5o

Resolution: 2.06→90.191 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.936 / WR_factor R_free: 0.241 / WR_factor R_work: 0.213 / SU B: 15.534 / SU ML: 0.195 / Average fsc free: 0.8258 / Average fsc work: 0.8337 / Cross valid method: FREE R-VALUE / ESU R: 0.219 / ESU R Free: 0.177
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2399	13971	4.972 %
R_work	0.2122	267014	-
all	0.214	-	-
obs	-	280985	98.228 %

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: 44.862 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.755 Å²	0.496 Å²	-0.979 Å²
2-	-	-0.093 Å²	0.21 Å²
3-	-	-	-1.595 Å²

Refinement step

Cycle: LAST / Resolution: 2.06→90.191 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	31476	0	96	1029	32601

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.013	32430
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	29276
X-RAY DIFFRACTION	r_angle_refined_deg	1.613	1.637	43882
X-RAY DIFFRACTION	r_angle_other_deg	1.368	1.573	68219
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.739	5	3901
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.764	23.917	1621
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.356	15	5524
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	24.434	15	90
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	4178
X-RAY DIFFRACTION	r_chiral_restr_other	0.081	0.2	6
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	35983
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	6940
X-RAY DIFFRACTION	r_nbd_refined	0.204	0.2	6216
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.189	0.2	26866
X-RAY DIFFRACTION	r_nbtor_refined	0.175	0.2	15525
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	13602
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.148	0.2	1215
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.125	0.2	16
X-RAY DIFFRACTION	r_nbd_other	0.239	0.2	65
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.184	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	1.799	2.397	15637
X-RAY DIFFRACTION	r_mcbond_other	1.799	2.396	15636
X-RAY DIFFRACTION	r_mcangle_it	2.875	3.585	19527
X-RAY DIFFRACTION	r_mcangle_other	2.875	3.585	19528
X-RAY DIFFRACTION	r_scbond_it	1.879	2.597	16793
X-RAY DIFFRACTION	r_scbond_other	1.879	2.597	16794
X-RAY DIFFRACTION	r_scangle_it	3.123	3.795	24355
X-RAY DIFFRACTION	r_scangle_other	3.123	3.795	24356
X-RAY DIFFRACTION	r_lrange_it	5.166	26.894	36311
X-RAY DIFFRACTION	r_lrange_other	5.158	26.784	36143
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.073	0.05	22512
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.074	0.05	22338
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.073	0.05	22395
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.078	0.05	22268
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.073	0.05	22275
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.071	0.05	22403
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.072	0.05	22421
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.074	0.05	22405
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.073	0.05	22352
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.079	0.05	22383
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.071	0.05	22400
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.073	0.05	22393
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.075	0.05	22437
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.075	0.05	22396
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.073	0.05	22434

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 (%)
2.06-2.113	0.377	1024	0.37	19574	X-RAY DIFFRACTION	97.2705
2.113-2.171	0.326	1046	0.323	19025	X-RAY DIFFRACTION	97.451
2.171-2.234	0.306	933	0.305	18600	X-RAY DIFFRACTION	97.3535
2.234-2.303	0.338	971	0.332	18031	X-RAY DIFFRACTION	97.5412
2.303-2.379	0.296	927	0.269	17525	X-RAY DIFFRACTION	97.8574
2.379-2.462	0.297	845	0.255	17002	X-RAY DIFFRACTION	97.8347
2.462-2.555	0.277	856	0.252	16483	X-RAY DIFFRACTION	98.1434
2.555-2.659	0.269	852	0.234	15798	X-RAY DIFFRACTION	98.3694
2.659-2.777	0.269	819	0.229	15211	X-RAY DIFFRACTION	98.4704
2.777-2.913	0.265	755	0.217	14597	X-RAY DIFFRACTION	98.5176
2.913-3.07	0.248	698	0.211	13852	X-RAY DIFFRACTION	98.711
3.07-3.257	0.24	717	0.208	13081	X-RAY DIFFRACTION	98.8112
3.257-3.481	0.255	654	0.218	12368	X-RAY DIFFRACTION	98.7787
3.481-3.76	0.22	634	0.201	11445	X-RAY DIFFRACTION	99.065
3.76-4.119	0.184	553	0.169	10594	X-RAY DIFFRACTION	99.1638
4.119-4.605	0.169	489	0.14	9610	X-RAY DIFFRACTION	99.2433
4.605-5.316	0.176	411	0.14	8499	X-RAY DIFFRACTION	99.1322
5.316-6.51	0.199	363	0.168	7133	X-RAY DIFFRACTION	99.2453
6.51-9.199	0.183	282	0.161	5541	X-RAY DIFFRACTION	99.6236
9.199-90.191	0.204	142	0.195	3045	X-RAY DIFFRACTION	99.1599

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.1158	-0.0332	0.081	0.1197	-0.0687	0.4985	-0.2092	0.0325	0.0114	0.089	0.0986	0.0102	-0.2557	-0.006	0.1107	0.6176	0.056	-0.1528	0.1564	-0.023	0.0875	2.7696	0.7912	4.4177
2	0.0253	-0.0994	0.0704	0.445	-0.2656	0.434	-0.0291	0.0416	0.0115	0.062	-0.0843	-0.0108	-0.3048	0.0388	0.1133	0.4936	-0.1224	-0.0653	0.2105	0.0277	0.063	17.2417	-38.164	-62.6985
3	0.065	-0.0227	0.1187	0.0726	-0.1618	0.5319	-0.1175	-0.0689	-0.0101	0.0563	0.0496	-0.0491	-0.1248	-0.0383	0.0679	0.4677	0.2727	-0.0347	0.2805	-0.0189	0.0531	16.9328	-31.4617	42.3818
4	0.1757	-0.066	0.0552	0.1007	0.014	0.2598	-0.1049	0.0306	-0.0119	0.0288	0.0828	0.0201	0.0675	-0.0297	0.0221	0.3792	0.0274	0.0059	0.1911	-0.0241	0.1811	-7.098	-49.9637	0.6417
5	0.0317	-0.0699	0.085	0.2169	-0.2485	0.3894	0.0374	0.0391	-0.0241	0.0553	-0.153	0.0263	-0.0483	0.1932	0.1155	0.1817	-0.1151	-0.0694	0.3764	0.0586	0.2247	32.5819	-84.6837	-45.4024
6	0.0971	-0.198	0.0027	0.4583	-0.1432	0.5466	0.1026	-0.0289	-0.0688	-0.2916	-0.0179	0.1855	0.0706	0.0661	-0.0847	0.3658	0.0165	-0.1947	0.2925	-0.015	0.1095	9.5879	-80.8345	-91.4528

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A*	25 - 801
2	X-RAY DIFFRACTION	2	ALL	D*	25 - 801
3	X-RAY DIFFRACTION	3	ALL	C*	32 - 801
4	X-RAY DIFFRACTION	4	ALL	B*	31 - 801
5	X-RAY DIFFRACTION	5	ALL	F*	30 - 801
6	X-RAY DIFFRACTION	6	ALL	E*	31 - 801

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