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- PDB-6f8z: Structure of the family GH92 alpha-mannosidase BT3130 from Bacter... -

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Basic information

Entry
Database: PDB / ID: 6f8z
TitleStructure of the family GH92 alpha-mannosidase BT3130 from Bacteroides thetaiotaomicron
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
GH92 family glycosyl hydrolase / Alpha-1,2-mannosidase, putative
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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
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.ptnr3_auth_seq_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)248,5567
Polymers248,3743
Non-polymers1824
Water23,2931293
1
A: Alpha-1,2-mannosidase, putative
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)165,7876
Polymers165,5832
Non-polymers2044
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z1
Buried area3710 Å2
ΔGint-24 kcal/mol
Surface area43770 Å2
MethodPISA
2
B: Alpha-1,2-mannosidase, putative
C: Alpha-1,2-mannosidase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,6634
Polymers165,5832
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-31 kcal/mol
Surface area43820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)272.301, 272.301, 190.047
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1293 / 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: 4.08 Å3/Da / Density % sol: 69.9 %
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: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.5→49.67 Å / Num. obs: 142171 / % possible obs: 99.8 % / Redundancy: 25 % / Biso Wilson estimate: 33.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.21 / Rpim(I) all: 0.06 / Rrim(I) all: 0.218 / Net I/σ(I): 18.6
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 24.5 % / Rmerge(I) obs: 2 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 6722 / CC1/2: 0.735 / Rpim(I) all: 0.579 / Rrim(I) all: 2.09 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WVY

2wvy


Resolution: 2.5→49.67 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.929 / SU B: 7.435 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.245 / ESU R Free: 0.206 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22176 7011 4.9 %RANDOM
Rwork0.18056 ---
obs0.1826 135113 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 50.745 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20.56 Å20 Å2
2--1.12 Å20 Å2
3----3.64 Å2
Refinement stepCycle: 1 / Resolution: 2.5→49.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16609 0 7 1293 17909
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01917207
X-RAY DIFFRACTIONr_bond_other_d0.0020.0215135
X-RAY DIFFRACTIONr_angle_refined_deg1.3181.91923399
X-RAY DIFFRACTIONr_angle_other_deg0.961334668
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.48652133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.16424.002852
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.634152535
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6871580
X-RAY DIFFRACTIONr_chiral_restr0.080.22424
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02120097
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024363
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_it2.5325.1988508
X-RAY DIFFRACTIONr_mcbond_other2.5285.1978503
X-RAY DIFFRACTIONr_mcangle_it4.0487.78410612
X-RAY DIFFRACTIONr_mcangle_other4.0487.78410613
X-RAY DIFFRACTIONr_scbond_it2.2825.2448699
X-RAY DIFFRACTIONr_scbond_other2.2825.2448699
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7257.81212779
X-RAY DIFFRACTIONr_long_range_B_refined6.10741.25720357
X-RAY DIFFRACTIONr_long_range_B_other6.10741.25720358
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.498→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 478 -
Rwork0.286 9662 -
obs--97.55 %

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