PDB-6f91: Structure of the family GH92 alpha-mannosidase BT3965 from Bacter...

ID or keywords:

Entry

Database: PDB / ID: 6f91

Title

Structure of the family GH92 alpha-mannosidase BT3965 from Bacteroides thetaiotaomicron

Components

Putative alpha-1,2-mannosidase

Keywords

HYDROLASE / glycan / carbohydrate / glycosidase / substrate specificity / glycoside hydrolase / alpha-mannosidase / GH92 / gut bacteria / microbiota / CAZy / CAZypedia

Function / homology

Function and homology information

carbohydrate binding / carbohydrate metabolic process / hydrolase activity
Similarity search - Function

Biological species

Bacteroides thetaiotaomicron (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Thompson, A.J. / Spears, R.J. / Zhu, Y. / Suits, M.D.L. / Williams, S.J. / Gilbert, H.J. / Davies, G.J.

Funding support

United Kingdom, 2items

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Bacteroides thetaiotaomicron generates diverse alpha-mannosidase activities through subtle evolution of a distal substrate-binding motif.
Authors: Thompson, A.J. / Spears, R.J. / Zhu, Y. / Suits, M.D.L. / Williams, S.J. / Gilbert, H.J. / Davies, G.J.

History

Deposition	Dec 13, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 2, 2018	Provider: repository / Type: Initial release
Revision 1.1	May 9, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Jan 17, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6f91.cif.gz	1.3 MB	Display	PDBx/mmCIF format
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Validation report

Summary document	6f91_validation.pdf.gz	520.6 KB	Display	wwPDB validaton report
Full document	6f91_full_validation.pdf.gz	564.9 KB	Display
Data in XML	6f91_validation.xml.gz	267.7 KB	Display
Data in CIF	6f91_validation.cif.gz	413 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f9/6f91 ftp://data.pdbj.org/pub/pdb/validation_reports/f9/6f91	HTTPS FTP

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Related structure data

Related structure data	6f8zC 6f90C 6f92C 2wvyS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4n2m-1 4n25-1 4n2h-1 6f92-1 4n24-1 1qdl-1 6f92-2 4n2f-1 4n2d-1 3dpn-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#198 - Jun 2016 Beta-galactosidase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #74 - Feb 2006 alpha-Amylase similarity (1)

Deposited unit

A: Putative alpha-1,2-mannosidase

B: Putative alpha-1,2-mannosidase

C: Putative alpha-1,2-mannosidase

D: Putative alpha-1,2-mannosidase

E: Putative alpha-1,2-mannosidase

F: Putative alpha-1,2-mannosidase

G: Putative alpha-1,2-mannosidase

H: Putative alpha-1,2-mannosidase

hetero molecules

703 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Putative alpha-1,2-mannosidase

hetero molecules

H: Putative alpha-1,2-mannosidase

hetero molecules

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

2

B: Putative alpha-1,2-mannosidase

E: Putative alpha-1,2-mannosidase

hetero molecules

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

3

D: Putative alpha-1,2-mannosidase

hetero molecules

C: Putative alpha-1,2-mannosidase

hetero molecules

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

4

F: Putative alpha-1,2-mannosidase

G: Putative alpha-1,2-mannosidase

hetero molecules

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

5

H: Putative alpha-1,2-mannosidase

hetero molecules

A: Putative alpha-1,2-mannosidase

hetero molecules

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

6

C: Putative alpha-1,2-mannosidase

hetero molecules

D: Putative alpha-1,2-mannosidase

hetero molecules

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

Unit cell

Length a, b, c (Å)	111.919, 184.542, 183.661
Angle α, β, γ (deg.)	90.00, 90.80, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLU	GLU	LEU	LEU	A	A	5 - 757	5 - 757
2	1	GLU	GLU	LEU	LEU	B	B	5 - 757	5 - 757
1	2	THR	THR	GLU	GLU	A	A	4 - 758	4 - 758
2	2	THR	THR	GLU	GLU	C	C	4 - 758	4 - 758
1	3	GLU	GLU	LEU	LEU	A	A	5 - 757	5 - 757
2	3	GLU	GLU	LEU	LEU	D	D	5 - 757	5 - 757
1	4	GLU	GLU	LEU	LEU	A	A	5 - 757	5 - 757
2	4	GLU	GLU	LEU	LEU	E	E	5 - 757	5 - 757
1	5	GLU	GLU	LEU	LEU	A	A	5 - 757	5 - 757
2	5	GLU	GLU	LEU	LEU	F	F	5 - 757	5 - 757
1	6	GLU	GLU	LEU	LEU	A	A	5 - 757	5 - 757
2	6	GLU	GLU	LEU	LEU	G	G	5 - 757	5 - 757
1	7	GLU	GLU	LEU	LEU	A	A	5 - 757	5 - 757
2	7	GLU	GLU	LEU	LEU	H	H	5 - 757	5 - 757
1	8	GLU	GLU	HIS	HIS	B	B	5 - 759	5 - 759
2	8	GLU	GLU	HIS	HIS	C	C	5 - 759	5 - 759
1	9	GLU	GLU	GLU	GLU	B	B	5 - 758	5 - 758
2	9	GLU	GLU	GLU	GLU	D	D	5 - 758	5 - 758
1	10	GLU	GLU	GLU	GLU	B	B	5 - 758	5 - 758
2	10	GLU	GLU	GLU	GLU	E	E	5 - 758	5 - 758
1	11	GLU	GLU	HIS	HIS	B	B	5 - 759	5 - 759
2	11	GLU	GLU	HIS	HIS	F	F	5 - 759	5 - 759
1	12	GLU	GLU	GLU	GLU	B	B	5 - 758	5 - 758
2	12	GLU	GLU	GLU	GLU	G	G	5 - 758	5 - 758
1	13	GLU	GLU	GLU	GLU	B	B	5 - 758	5 - 758
2	13	GLU	GLU	GLU	GLU	H	H	5 - 758	5 - 758
1	14	GLU	GLU	HIS	HIS	C	C	5 - 759	5 - 759
2	14	GLU	GLU	HIS	HIS	D	D	5 - 759	5 - 759
1	15	GLU	GLU	HIS	HIS	C	C	5 - 759	5 - 759
2	15	GLU	GLU	HIS	HIS	E	E	5 - 759	5 - 759
1	16	GLU	GLU	HIS	HIS	C	C	5 - 759	5 - 759
2	16	GLU	GLU	HIS	HIS	F	F	5 - 759	5 - 759
1	17	GLU	GLU	HIS	HIS	C	C	5 - 759	5 - 759
2	17	GLU	GLU	HIS	HIS	G	G	5 - 759	5 - 759
1	18	GLU	GLU	HIS	HIS	C	C	5 - 759	5 - 759
2	18	GLU	GLU	HIS	HIS	H	H	5 - 759	5 - 759
1	19	GLU	GLU	HIS	HIS	D	D	5 - 764	5 - 764
2	19	GLU	GLU	HIS	HIS	E	E	5 - 764	5 - 764
1	20	GLU	GLU	GLU	GLU	D	D	5 - 758	5 - 758
2	20	GLU	GLU	GLU	GLU	F	F	5 - 758	5 - 758
1	21	GLU	GLU	HIS	HIS	D	D	5 - 764	5 - 764
2	21	GLU	GLU	HIS	HIS	G	G	5 - 764	5 - 764
1	22	GLU	GLU	HIS	HIS	D	D	5 - 764	5 - 764
2	22	GLU	GLU	HIS	HIS	H	H	5 - 764	5 - 764
1	23	GLU	GLU	GLU	GLU	E	E	5 - 758	5 - 758
2	23	GLU	GLU	GLU	GLU	F	F	5 - 758	5 - 758
1	24	GLU	GLU	HIS	HIS	E	E	5 - 764	5 - 764
2	24	GLU	GLU	HIS	HIS	G	G	5 - 764	5 - 764
1	25	GLU	GLU	HIS	HIS	E	E	5 - 764	5 - 764
2	25	GLU	GLU	HIS	HIS	H	H	5 - 764	5 - 764
1	26	GLU	GLU	GLU	GLU	F	F	5 - 758	5 - 758
2	26	GLU	GLU	GLU	GLU	G	G	5 - 758	5 - 758
1	27	GLU	GLU	GLU	GLU	F	F	5 - 758	5 - 758
2	27	GLU	GLU	GLU	GLU	H	H	5 - 758	5 - 758
1	28	GLU	GLU	HIS	HIS	G	G	5 - 764	5 - 764
2	28	GLU	GLU	HIS	HIS	H	H	5 - 764	5 - 764

NCS ensembles :

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein	Putative alpha-1,2-mannosidase Mass: 87566.141 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Gene: HMPREF2534_04919 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): TUNER / References: UniProt: A0A139JT15, UniProt: Q8A0Q6*PLUS

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Non-polymers , 5 types, 6809 molecules

#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 6759 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.71 Å³/Da / Density % sol: 54.57 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20% w/v PEG 3350, 0.2 M NaNO3

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97949 Å / Relative weight: 1
Reflection	Resolution: 1.8→48.08 Å / Num. obs: 682384 / % possible obs: 99.5 % / Redundancy: 4.2 % / B_iso Wilson estimate: 16.9 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.086 / R_pim(I) all: 0.073 / R_rim(I) all: 0.114 / Net I/σ(I): 10.4
Reflection shell	Resolution: 1.8→1.83 Å / Redundancy: 4.1 % / R_merge(I) obs: 0.983 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 32477 / CC_1/2: 0.672 / R_pim(I) all: 0.837 / R_rim(I) all: 1.296 / % possible all: 95.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0189	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2WVY

2wvy

Resolution: 1.8→48.08 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.96 / SU B: 2.642 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.099 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18522	33861	5 %	RANDOM
R_work	0.15984	-	-	-
obs	0.16109	648458	99.46 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 27.431 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.93 Å²	0 Å²	-0.14 Å²
2-	-	-1.68 Å²	0 Å²
3-	-	-	-2.24 Å²

Refinement step

Cycle: 1 / Resolution: 1.8→48.08 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	47560	0	128	6759	54447

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.019	49802
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	43436
X-RAY DIFFRACTION	r_angle_refined_deg	1.526	1.936	67542
X-RAY DIFFRACTION	r_angle_other_deg	0.987	3	100946
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.805	5	6113
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.021	23.84	2445
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.742	15	7954
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.724	15	249
X-RAY DIFFRACTION	r_chiral_restr	0.106	0.2	6933
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	56085
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	11056
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	2.118	2.55	23958
X-RAY DIFFRACTION	r_mcbond_other	2.116	2.55	23952
X-RAY DIFFRACTION	r_mcangle_it	2.848	3.805	29916
X-RAY DIFFRACTION	r_mcangle_other	2.848	3.805	29917
X-RAY DIFFRACTION	r_scbond_it	2.811	2.81	25844
X-RAY DIFFRACTION	r_scbond_other	2.811	2.81	25844
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	4.192	4.107	37528
X-RAY DIFFRACTION	r_long_range_B_refined	6.066	31.052	60697
X-RAY DIFFRACTION	r_long_range_B_other	6.066	31.052	60698
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	53060	0.04
1	2	B	53060	0.04
2	1	A	53018	0.04
2	2	C	53018	0.04
3	1	A	52514	0.05
3	2	D	52514	0.05
4	1	A	52780	0.05
4	2	E	52780	0.05
5	1	A	52844	0.04
5	2	F	52844	0.04
6	1	A	52732	0.05
6	2	G	52732	0.05
7	1	A	52754	0.05
7	2	H	52754	0.05
8	1	B	53252	0.04
8	2	C	53252	0.04
9	1	B	52616	0.05
9	2	D	52616	0.05
10	1	B	52964	0.05
10	2	E	52964	0.05
11	1	B	52904	0.05
11	2	F	52904	0.05
12	1	B	52738	0.05
12	2	G	52738	0.05
13	1	B	52910	0.05
13	2	H	52910	0.05
14	1	C	52960	0.05
14	2	D	52960	0.05
15	1	C	52942	0.05
15	2	E	52942	0.05
16	1	C	52908	0.04
16	2	F	52908	0.04
17	1	C	52814	0.06
17	2	G	52814	0.06
18	1	C	52870	0.05
18	2	H	52870	0.05
19	1	D	53796	0.04
19	2	E	53796	0.04
20	1	D	52670	0.05
20	2	F	52670	0.05
21	1	D	53530	0.05
21	2	G	53530	0.05
22	1	D	53438	0.05
22	2	H	53438	0.05
23	1	E	52930	0.05
23	2	F	52930	0.05
24	1	E	53862	0.04
24	2	G	53862	0.04
25	1	E	53716	0.05
25	2	H	53716	0.05
26	1	F	52480	0.05
26	2	G	52480	0.05
27	1	F	52468	0.05
27	2	H	52468	0.05
28	1	G	53830	0.04
28	2	H	53830	0.04

LS refinement shell

Resolution: 1.8→1.847 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.298	2545	-
R_work	0.287	46741	-
obs	-	-	97.19 %

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Protein , 1 types, 8 molecules ABCDEFGH

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Non-polymers , 5 types, 6809 molecules

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Processing

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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