PDB-6t75: Bacteroides salyersiae GH164 beta-mannosidase 2-deoxy-2-fluoro-be...

ID or keywords:

Entry

Database: PDB / ID: 6t75

Title

Bacteroides salyersiae GH164 beta-mannosidase 2-deoxy-2-fluoro-beta-D-mannosyl enzyme intermediate

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 / 2-deoxy-2-fluoro-alpha-D-mannopyranose / Beta-galactosidase trimerisation domain-containing protein

Function and homology information

Biological species

Bacteroides salyersiae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.55 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 21, 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 2.0	Jul 29, 2020	Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1	Jan 24, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: atom_type / chem_comp ...atom_type / chem_comp / 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 / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6t75.cif.gz	2.5 MB	Display	PDBx/mmCIF format
PDB format	pdb6t75.ent.gz		Display	PDB format
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Validation report

Summary document	6t75_validation.pdf.gz	2.3 MB	Display	wwPDB validaton report
Full document	6t75_full_validation.pdf.gz	2.3 MB	Display
Data in XML	6t75_validation.xml.gz	125.2 KB	Display
Data in CIF	6t75_validation.cif.gz	171.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t7/6t75 ftp://data.pdbj.org/pub/pdb/validation_reports/t7/6t75	HTTPS FTP

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Related structure data

Related structure data	6t5oC 6t6gC 6t7gC 6t50S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6t75-2 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

461 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, Trimer
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)	70.155, 104.873, 171.627
Angle α, β, γ (deg.)	91.977, 97.733, 107.161
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	2	Chains A C
3	3	Chains A B
4	4	Chains A F
5	5	Chains A E
6	6	Chains D C
7	7	Chains D B
8	8	Chains D F
9	9	Chains D E
10	10	Chains C B
11	11	Chains C F
12	12	Chains C E
13	13	Chains B F
14	14	Chains B E
15	15	Chains F E

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

#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: Sugar

ChemComp-MAF / 2-deoxy-2-fluoro-alpha-D-mannopyranose / 2-DEOXY-2-FLUORO-ALPHA-D-MANNOSE / 2-deoxy-2-fluoro-D-mannose / 2-deoxy-2-fluoro-mannose

Type: D-saccharide, alpha linking / Mass: 182.147 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₆H₁₁FO₅ / Feature type: SUBJECT OF INVESTIGATION

#3: Chemical

ChemComp-CL / CHLORIDE ION

Mass: 35.453 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: Cl

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 157 / 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: 52.52 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: Ammonium tartrate, PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 15, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97625 Å / Relative weight: 1
Reflection	Resolution: 2.55→99.9 Å / Num. obs: 148606 / % possible obs: 98.7 % / Redundancy: 3.6 % / CC_1/2: 0.994 / Net I/σ(I): 6.1
Reflection shell	Resolution: 2.55→2.59 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 7334 / CC_1/2: 0.458

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6T50

6t50

Resolution: 2.55→89.337 Å / Cor.coef. F_o:F_c: 0.922 / Cor.coef. F_o:F_c free: 0.907 / WR_factor R_free: 0.235 / WR_factor R_work: 0.204 / SU B: 31.259 / SU ML: 0.289 / Average fsc free: 0.8539 / Average fsc work: 0.8632 / Cross valid method: FREE R-VALUE / ESU R: 0.821 / ESU R Free: 0.303
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2452	7529	5.067 %
R_work	0.2138	141046	-
all	0.215	-	-
obs	-	148575	98.643 %

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: 49.969 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.778 Å²	-0.942 Å²	-0.34 Å²
2-	-	-0.228 Å²	0.413 Å²
3-	-	-	-1.823 Å²

Refinement step

Cycle: LAST / Resolution: 2.55→89.337 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	31388	0	72	157	31617

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	32320
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	29140
X-RAY DIFFRACTION	r_angle_refined_deg	1.548	1.64	43755
X-RAY DIFFRACTION	r_angle_other_deg	1.255	1.575	67918
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.575	5	3886
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.326	23.947	1614
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.894	15	5504
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.419	15	88
X-RAY DIFFRACTION	r_chiral_restr	0.068	0.2	4175
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	35850
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	6911
X-RAY DIFFRACTION	r_nbd_refined	0.195	0.2	5703
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.177	0.2	25271
X-RAY DIFFRACTION	r_nbtor_refined	0.17	0.2	15294
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.077	0.2	13935
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.126	0.2	481
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.016	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.171	0.2	16
X-RAY DIFFRACTION	r_nbd_other	0.241	0.2	73
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.253	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	2.437	4.087	15586
X-RAY DIFFRACTION	r_mcbond_other	2.436	4.087	15585
X-RAY DIFFRACTION	r_mcangle_it	3.862	6.126	19458
X-RAY DIFFRACTION	r_mcangle_other	3.861	6.126	19459
X-RAY DIFFRACTION	r_scbond_it	2.468	4.307	16734
X-RAY DIFFRACTION	r_scbond_other	2.467	4.307	16734
X-RAY DIFFRACTION	r_scangle_it	4.045	6.346	24297
X-RAY DIFFRACTION	r_scangle_other	4.045	6.346	24298
X-RAY DIFFRACTION	r_lrange_it	5.741	45.319	34858
X-RAY DIFFRACTION	r_lrange_other	5.741	45.32	34858
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.073	0.05	21793
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.071	0.05	21686
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.07	0.05	21656
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.068	0.05	21739
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.071	0.05	21493
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.071	0.05	21564
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.071	0.05	21499
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.071	0.05	21560
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.07	0.05	21406
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.071	0.05	21643
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.072	0.05	21706
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.072	0.05	21477
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.072	0.05	21713
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.074	0.05	21485
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.071	0.05	21484

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 (%)
2.55-2.616	0.353	515	0.334	10410	X-RAY DIFFRACTION	97.8329
2.616-2.688	0.339	514	0.318	10175	X-RAY DIFFRACTION	98.0552
2.688-2.766	0.322	553	0.296	9751	X-RAY DIFFRACTION	98.1707
2.766-2.851	0.309	501	0.277	9552	X-RAY DIFFRACTION	98.2986
2.851-2.944	0.285	507	0.268	9276	X-RAY DIFFRACTION	98.3612
2.944-3.048	0.292	506	0.249	9034	X-RAY DIFFRACTION	98.4927
3.048-3.163	0.283	431	0.245	8708	X-RAY DIFFRACTION	98.417
3.163-3.292	0.272	416	0.222	8322	X-RAY DIFFRACTION	98.5007
3.292-3.438	0.249	398	0.215	8027	X-RAY DIFFRACTION	98.7459
3.438-3.606	0.239	437	0.201	7662	X-RAY DIFFRACTION	98.8406
3.606-3.801	0.237	358	0.193	7362	X-RAY DIFFRACTION	98.949
3.801-4.031	0.222	345	0.173	6934	X-RAY DIFFRACTION	99.0745
4.031-4.309	0.192	372	0.153	6500	X-RAY DIFFRACTION	99.1917
4.309-4.654	0.176	327	0.142	6076	X-RAY DIFFRACTION	99.2713
4.654-5.098	0.172	365	0.147	5501	X-RAY DIFFRACTION	99.3059
5.098-5.699	0.217	286	0.177	5029	X-RAY DIFFRACTION	99.4387
5.699-6.58	0.245	243	0.194	4450	X-RAY DIFFRACTION	99.428
6.58-8.055	0.219	209	0.208	3766	X-RAY DIFFRACTION	99.649
8.055-11.379	0.262	156	0.219	2918	X-RAY DIFFRACTION	99.6757
11.379-89.337	0.335	90	0.347	1593	X-RAY DIFFRACTION	99.3506

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	0.101	0.0074	-0.0001	0.1786	0.1129	0.4149	-0.0307	0.0392	0.0133	0.0045	0.0349	0.0334	-0.1386	0.0329	-0.0042	0.2538	0.0038	0.0215	0.0235	0.0122	0.1115	44.0283	101.61	3.7624
2	0.0886	0.0414	-0.0069	0.0858	0.0334	0.6005	0.0565	0.0096	0.002	0.0113	0.0179	-0.0034	-0.2248	-0.0528	-0.0744	0.2883	-0.0101	0.0913	0.0489	-0.0051	0.0322	59.7936	63.8616	-62.436
3	0.0263	0.0426	-0.0101	0.2457	-0.0874	0.3303	-0.0357	-0.0165	-0.0218	0.0468	0.0389	0.0277	-0.0327	0.0759	-0.0032	0.1732	0.0729	0.0408	0.0841	0.0068	0.1028	58.3319	69.8097	42.4814
4	0.137	-0.0728	0.0561	0.2591	-0.0963	0.1633	-0.0595	0.0223	-0.0273	-0.0125	0.0322	0.0433	0.0459	-0.0128	0.0272	0.1725	0.0217	0.0349	0.0505	-0.0094	0.1352	34.3477	50.3887	0.6572
5	0.0681	0.0279	-0.0273	0.3488	-0.2787	0.2966	0.0558	-0.0889	-0.0263	-0.0631	-0.0969	-0.0029	0.0129	0.0739	0.0411	0.1037	-0.0427	-0.0044	0.1396	0.016	0.101	76.712	17.6828	-45.1845
6	0.0735	-0.0914	-0.0065	0.1671	0.0283	0.397	0.0014	0.0266	-0.0095	-0.0621	0.0453	-0.0076	0.0417	-0.0625	-0.0467	0.2086	-0.0585	-0.025	0.1622	-0.0363	0.0244	54.8688	21.1406	-92.5272

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	24 - 701
2	X-RAY DIFFRACTION	2	ALL	DDD	25 - 701
3	X-RAY DIFFRACTION	3	ALL	CCC	32 - 701
4	X-RAY DIFFRACTION	4	ALL	BBB	31 - 701
5	X-RAY DIFFRACTION	5	ALL	FFF	30 - 701
6	X-RAY DIFFRACTION	6	ALL	EEE	31 - 701

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