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- PDB-6f90: Structure of the family GH92 alpha-mannosidase BT3130 from Bacter... -

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Basic information

Entry
Database: PDB / ID: 6f90
TitleStructure of the family GH92 alpha-mannosidase BT3130 from Bacteroides thetaiotaomicron in complex with Mannoimidazole (ManI)
ComponentsAlpha-1,2-mannosidase, putative
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 / hydrolase activity, acting on glycosyl bonds / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / 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
Chem-MVL / GH92 family glycosyl hydrolase / Alpha-1,2-mannosidase, putative
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 / pdbx_struct_special_symmetry / struct_conn
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-1,2-mannosidase, putative
B: Alpha-1,2-mannosidase, putative
C: Alpha-1,2-mannosidase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,0959
Polymers248,3743
Non-polymers7216
Water21,3481185
1
A: Alpha-1,2-mannosidase, putative
hetero molecules

A: Alpha-1,2-mannosidase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,0636
Polymers165,5832
Non-polymers4814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z1
Buried area3190 Å2
ΔGint-34 kcal/mol
Surface area42970 Å2
MethodPISA
2
B: Alpha-1,2-mannosidase, putative
C: Alpha-1,2-mannosidase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,0636
Polymers165,5832
Non-polymers4814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-37 kcal/mol
Surface area42810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)273.666, 273.666, 189.759
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-1479-

HOH

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Components

#1: Protein Alpha-1,2-mannosidase, putative / Glycoside hydrolase


Mass: 82791.266 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: ERS852430_04477, ERS852511_01397, SAMN02910322_03319 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): TUNER / References: UniProt: A0A174L250, UniProt: Q8A325*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MVL / (5R,6R,7S,8R)-5-(HYDROXYMETHYL)-5,6,7,8-TETRAHYDROIMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL / Mannoimidazole


Mass: 200.192 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H12N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1185 / 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: 4.23 Å3/Da / Density % sol: 70.95 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 18% (w/v) PEG 3350, 0.1 M Bis-Tris propane, pH 6.4, 0.2 M NaBr

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→49.38 Å / Num. obs: 160656 / % possible obs: 99.5 % / Redundancy: 25.1 % / Biso Wilson estimate: 40.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.195 / Rpim(I) all: 0.056 / Rrim(I) all: 0.203 / Net I/σ(I): 18.4
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 25.9 % / Rmerge(I) obs: 2.48 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 7817 / CC1/2: 0.661 / Rpim(I) all: 0.702 / Rrim(I) all: 2.58 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WVY

2wvy


Resolution: 2.4→49.38 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.923 / SU B: 7.441 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.235 / ESU R Free: 0.202 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24227 7949 4.9 %RANDOM
Rwork0.20722 ---
obs0.20895 152705 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 62.755 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20.53 Å20 Å2
2--1.06 Å20 Å2
3----3.42 Å2
Refinement stepCycle: 1 / Resolution: 2.4→49.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16403 0 45 1185 17633
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01916987
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214767
X-RAY DIFFRACTIONr_angle_refined_deg1.2671.92123116
X-RAY DIFFRACTIONr_angle_other_deg0.949333829
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.49952114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.11324.066824
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.961152425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2671572
X-RAY DIFFRACTIONr_chiral_restr0.0770.22414
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02119858
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024282
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_it3.0846.558465
X-RAY DIFFRACTIONr_mcbond_other3.0786.5488461
X-RAY DIFFRACTIONr_mcangle_it4.919.8110558
X-RAY DIFFRACTIONr_mcangle_other4.919.81110559
X-RAY DIFFRACTIONr_scbond_it2.5636.5368522
X-RAY DIFFRACTIONr_scbond_other2.5636.5368523
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1759.76412555
X-RAY DIFFRACTIONr_long_range_B_refined7.52651.74520298
X-RAY DIFFRACTIONr_long_range_B_other7.4651.73919854
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 594 -
Rwork0.316 11113 -
obs--98.89 %

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