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

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Basic information

Entry
Database: PDB / ID: 6f91
TitleStructure of the family GH92 alpha-mannosidase BT3965 from Bacteroides thetaiotaomicron
ComponentsPutative alpha-1,2-mannosidase
KeywordsHYDROLASE / glycan / carbohydrate / glycosidase / substrate specificity / glycoside hydrolase / alpha-mannosidase / GH92 / gut bacteria / microbiota / CAZy / CAZypedia
Function / homology
Function and homology information


peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity / glycoprotein catabolic process / carbohydrate binding / carbohydrate metabolic process / metal ion binding / cytosol
Similarity search - Function
Alpha-1,2-mannosidase, putative / Glycosyl hydrolase family 92 / Glycosyl hydrolase family 92 N-terminal domain / Glycosyl hydrolase family 92 catalytic domain / Glycosyl hydrolase family 92 N-terminal domain / : / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Six-hairpin glycosidase superfamily ...Alpha-1,2-mannosidase, putative / Glycosyl hydrolase family 92 / Glycosyl hydrolase family 92 N-terminal domain / Glycosyl hydrolase family 92 catalytic domain / Glycosyl hydrolase family 92 N-terminal domain / : / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Six-hairpin glycosidase superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Glycoside hydrolase family 92 protein / Alpha-1,2-mannosidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsThompson, 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
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/G016127/1 United Kingdom
Royal SocietyKen Murray Research Professorship United Kingdom
CitationJournal: 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
DepositionDec 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: 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 1.2Jan 17, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)702,93158
Polymers700,5298
Non-polymers2,40250
Water121,7636759
1
A: Putative alpha-1,2-mannosidase
hetero molecules

H: Putative alpha-1,2-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,70214
Polymers175,1322
Non-polymers56912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y+1/2,-z+21
Buried area5270 Å2
ΔGint-62 kcal/mol
Surface area48760 Å2
MethodPISA
2
B: Putative alpha-1,2-mannosidase
E: Putative alpha-1,2-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,70214
Polymers175,1322
Non-polymers56912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-56 kcal/mol
Surface area48000 Å2
MethodPISA
3
D: Putative alpha-1,2-mannosidase
hetero molecules

C: Putative alpha-1,2-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,82616
Polymers175,1322
Non-polymers69414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_548-x,y-1/2,-z+31
Buried area6170 Å2
ΔGint-46 kcal/mol
Surface area48960 Å2
MethodPISA
4
F: Putative alpha-1,2-mannosidase
G: Putative alpha-1,2-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,70214
Polymers175,1322
Non-polymers56912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-63 kcal/mol
Surface area47780 Å2
MethodPISA
5
H: Putative alpha-1,2-mannosidase
hetero molecules

A: Putative alpha-1,2-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,70214
Polymers175,1322
Non-polymers56912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_547-x,y-1/2,-z+21
Buried area5270 Å2
ΔGint-62 kcal/mol
Surface area48760 Å2
MethodPISA
6
C: Putative alpha-1,2-mannosidase
hetero molecules

D: Putative alpha-1,2-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,82616
Polymers175,1322
Non-polymers69414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_558-x,y+1/2,-z+31
Buried area6170 Å2
ΔGint-46 kcal/mol
Surface area48960 Å2
MethodPISA
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 number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLULEULEUAA5 - 7575 - 757
21GLUGLULEULEUBB5 - 7575 - 757
12THRTHRGLUGLUAA4 - 7584 - 758
22THRTHRGLUGLUCC4 - 7584 - 758
13GLUGLULEULEUAA5 - 7575 - 757
23GLUGLULEULEUDD5 - 7575 - 757
14GLUGLULEULEUAA5 - 7575 - 757
24GLUGLULEULEUEE5 - 7575 - 757
15GLUGLULEULEUAA5 - 7575 - 757
25GLUGLULEULEUFF5 - 7575 - 757
16GLUGLULEULEUAA5 - 7575 - 757
26GLUGLULEULEUGG5 - 7575 - 757
17GLUGLULEULEUAA5 - 7575 - 757
27GLUGLULEULEUHH5 - 7575 - 757
18GLUGLUHISHISBB5 - 7595 - 759
28GLUGLUHISHISCC5 - 7595 - 759
19GLUGLUGLUGLUBB5 - 7585 - 758
29GLUGLUGLUGLUDD5 - 7585 - 758
110GLUGLUGLUGLUBB5 - 7585 - 758
210GLUGLUGLUGLUEE5 - 7585 - 758
111GLUGLUHISHISBB5 - 7595 - 759
211GLUGLUHISHISFF5 - 7595 - 759
112GLUGLUGLUGLUBB5 - 7585 - 758
212GLUGLUGLUGLUGG5 - 7585 - 758
113GLUGLUGLUGLUBB5 - 7585 - 758
213GLUGLUGLUGLUHH5 - 7585 - 758
114GLUGLUHISHISCC5 - 7595 - 759
214GLUGLUHISHISDD5 - 7595 - 759
115GLUGLUHISHISCC5 - 7595 - 759
215GLUGLUHISHISEE5 - 7595 - 759
116GLUGLUHISHISCC5 - 7595 - 759
216GLUGLUHISHISFF5 - 7595 - 759
117GLUGLUHISHISCC5 - 7595 - 759
217GLUGLUHISHISGG5 - 7595 - 759
118GLUGLUHISHISCC5 - 7595 - 759
218GLUGLUHISHISHH5 - 7595 - 759
119GLUGLUHISHISDD5 - 7645 - 764
219GLUGLUHISHISEE5 - 7645 - 764
120GLUGLUGLUGLUDD5 - 7585 - 758
220GLUGLUGLUGLUFF5 - 7585 - 758
121GLUGLUHISHISDD5 - 7645 - 764
221GLUGLUHISHISGG5 - 7645 - 764
122GLUGLUHISHISDD5 - 7645 - 764
222GLUGLUHISHISHH5 - 7645 - 764
123GLUGLUGLUGLUEE5 - 7585 - 758
223GLUGLUGLUGLUFF5 - 7585 - 758
124GLUGLUHISHISEE5 - 7645 - 764
224GLUGLUHISHISGG5 - 7645 - 764
125GLUGLUHISHISEE5 - 7645 - 764
225GLUGLUHISHISHH5 - 7645 - 764
126GLUGLUGLUGLUFF5 - 7585 - 758
226GLUGLUGLUGLUGG5 - 7585 - 758
127GLUGLUGLUGLUFF5 - 7585 - 758
227GLUGLUGLUGLUHH5 - 7585 - 758
128GLUGLUHISHISGG5 - 7645 - 764
228GLUGLUHISHISHH5 - 7645 - 764

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

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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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.57 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.8→48.08 Å / Num. obs: 682384 / % possible obs: 99.5 % / Redundancy: 4.2 % / Biso Wilson estimate: 16.9 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.073 / Rrim(I) all: 0.114 / Net I/σ(I): 10.4
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.983 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 32477 / CC1/2: 0.672 / Rpim(I) all: 0.837 / Rrim(I) all: 1.296 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WVY

2wvy


Resolution: 1.8→48.08 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc 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
RfactorNum. reflection% reflectionSelection details
Rfree0.18522 33861 5 %RANDOM
Rwork0.15984 ---
obs0.16109 648458 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.431 Å2
Baniso -1Baniso -2Baniso -3
1-3.93 Å20 Å2-0.14 Å2
2---1.68 Å20 Å2
3----2.24 Å2
Refinement stepCycle: 1 / Resolution: 1.8→48.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47560 0 128 6759 54447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01949802
X-RAY DIFFRACTIONr_bond_other_d0.0020.0243436
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.93667542
X-RAY DIFFRACTIONr_angle_other_deg0.9873100946
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.80556113
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.02123.842445
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.742157954
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.72415249
X-RAY DIFFRACTIONr_chiral_restr0.1060.26933
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02156085
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0211056
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1182.5523958
X-RAY DIFFRACTIONr_mcbond_other2.1162.5523952
X-RAY DIFFRACTIONr_mcangle_it2.8483.80529916
X-RAY DIFFRACTIONr_mcangle_other2.8483.80529917
X-RAY DIFFRACTIONr_scbond_it2.8112.8125844
X-RAY DIFFRACTIONr_scbond_other2.8112.8125844
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1924.10737528
X-RAY DIFFRACTIONr_long_range_B_refined6.06631.05260697
X-RAY DIFFRACTIONr_long_range_B_other6.06631.05260698
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A530600.04
12B530600.04
21A530180.04
22C530180.04
31A525140.05
32D525140.05
41A527800.05
42E527800.05
51A528440.04
52F528440.04
61A527320.05
62G527320.05
71A527540.05
72H527540.05
81B532520.04
82C532520.04
91B526160.05
92D526160.05
101B529640.05
102E529640.05
111B529040.05
112F529040.05
121B527380.05
122G527380.05
131B529100.05
132H529100.05
141C529600.05
142D529600.05
151C529420.05
152E529420.05
161C529080.04
162F529080.04
171C528140.06
172G528140.06
181C528700.05
182H528700.05
191D537960.04
192E537960.04
201D526700.05
202F526700.05
211D535300.05
212G535300.05
221D534380.05
222H534380.05
231E529300.05
232F529300.05
241E538620.04
242G538620.04
251E537160.05
252H537160.05
261F524800.05
262G524800.05
271F524680.05
272H524680.05
281G538300.04
282H538300.04
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 2545 -
Rwork0.287 46741 -
obs--97.19 %

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