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- PDB-2ww1: Structure of the Family GH92 Inverting Mannosidase BT3990 from Ba... -

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Basic information

Entry
Database: PDB / ID: 2ww1
TitleStructure of the Family GH92 Inverting Mannosidase BT3990 from Bacteroides thetaiotaomicron VPI-5482 in complex with Thiomannobioside
ComponentsPUTATIVE ALPHA-1,2-MANNOSIDASE
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE FAMILY 92 / GH92 / BT3990
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 / Glycosyl hydrolase family fold / alpha-1,2-mannosidases domains / GH92 mannosidase fold / GH92 mannosidase domain / 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 ...alpha-1,2-mannosidase / Glycosyl hydrolase family fold / alpha-1,2-mannosidases domains / GH92 mannosidase fold / GH92 mannosidase domain / 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 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Distorted Sandwich / Up-down Bundle / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
methyl 2-S-alpha-D-mannopyranosyl-2-thio-alpha-D-mannopyranoside / Alpha-1,2-mannosidase
Similarity search - Component
Biological speciesBACTEROIDES THETAIOTAOMICRON (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSuits, M.D.L. / Zhu, Y. / Thompson, A. / Gilbert, H.J. / Davies, G.J.
CitationJournal: Nat.Chem.Biol. / Year: 2010
Title: Mechanistic Insights Into a Ca2+-Dependent Family of A-Mannosidases in a Human Gut Symbiont.
Authors: Zhu, Y. / Suits, M.D.L. / Thompson, A. / Chavan, S. / Dinev, Z. / Dumon, C. / Smith, N. / Moremen, K.W. / Xiang, Y. / Siriwardena, A. / Williams, S.J. / Gilbert, H.J. / Davies, G.J.
History
DepositionOct 21, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)344,2538
Polymers342,7634
Non-polymers1,4904
Water24,5001360
1
A: PUTATIVE ALPHA-1,2-MANNOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0632
Polymers85,6911
Non-polymers3721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PUTATIVE ALPHA-1,2-MANNOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0632
Polymers85,6911
Non-polymers3721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PUTATIVE ALPHA-1,2-MANNOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0632
Polymers85,6911
Non-polymers3721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: PUTATIVE ALPHA-1,2-MANNOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0632
Polymers85,6911
Non-polymers3721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.240, 153.110, 185.210
Angle α, β, γ (deg.)90.00, 91.37, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TRP / Beg label comp-ID: TRP / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 3 / Auth seq-ID: 22 - 750 / Label seq-ID: 3 - 731

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

NCS oper: (Code: given)

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Components

#1: Protein
PUTATIVE ALPHA-1,2-MANNOSIDASE / MANNOSIDASE


Mass: 85690.859 Da / Num. of mol.: 4 / Fragment: RESIDUES 20-755
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria)
Strain: VPI-5482 / Plasmid: PET 22 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TUNER / References: UniProt: Q8A0N1
#2: Polysaccharide
alpha-D-mannopyranose-(1-2)-methyl 2-thio-alpha-D-mannopyranoside / methyl 2-S-alpha-D-mannopyranosyl-2-thio-alpha-D-mannopyranoside


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 372.389 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with S-glycosidic bond between monosaccharides
References: methyl 2-S-alpha-D-mannopyranosyl-2-thio-alpha-D-mannopyranoside
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a1122h-1a_1-5_1*OC][a1122h-1a_1-5]/1-2/a2-b1*S*WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][a-D-Manp2SH]{[(2+S)][a-D-Manp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1360 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsMETHYL-2-S-(ALPHA-D-MANNOPYRANOSYL)-2-THIO-ALPHA-D- MANNOPYRANOSIDE (SMD): THIOL LINKED MANNOBIOSE
Sequence detailsFIRST 19 RESIDUES WERE REMOVED DURING CLONING

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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: 2.75 Å3/Da / Density % sol: 55.4 % / Description: NONE
Crystal growDetails: 20% 3350 PEG, 0.1 M (4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID) (PH 7.0), 0.15 M K2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9762
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.25→44.6 Å / Num. obs: 174544 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 7.1
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.4.0077refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WVX

2wvx


Resolution: 2.25→185.16 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.906 / SU B: 11.86 / SU ML: 0.133 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.27 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE ONLY. U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21817 8730 5 %RANDOM
Rwork0.1875 ---
obs0.18904 165726 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.722 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20.02 Å2
2---0.93 Å20 Å2
3---0.86 Å2
Refinement stepCycle: LAST / Resolution: 2.25→185.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23863 0 96 1360 25319
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02224793
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2091.94133669
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.89652975
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.44924.4111274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.787153967
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.18815104
X-RAY DIFFRACTIONr_chiral_restr0.0830.23408
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02119520
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.4551.514703
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.885223723
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.583310090
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5894.59929
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2911tight positional0.040.05
2B2911tight positional0.040.05
3C2911tight positional0.040.05
4D2911tight positional0.040.05
1A2962loose positional0.045
2B2962loose positional0.045
3C2962loose positional0.045
4D2962loose positional0.045
1A2911tight thermal0.10.5
2B2911tight thermal0.10.5
3C2911tight thermal0.10.5
4D2911tight thermal0.090.5
1A2962loose thermal0.1110
2B2962loose thermal0.1210
3C2962loose thermal0.1110
4D2962loose thermal0.1110
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 662 -
Rwork0.278 12176 -
obs--99.82 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.34180.10690.22440.30730.13250.65890.0311-0.039-0.01180.0313-0.0040.01360.1106-0.0067-0.02710.0324-0.0055-0.00620.00390.00180.05742.2211-9.3067.2573
20.2556-0.08690.04520.2786-0.02310.2847-0.0056-0.0603-0.0260.02330.00290.0030.04030.06070.00270.01820.0212-0.01840.0446-0.00540.032428.352616.707334.0653
30.20350.0958-0.11530.32460.01180.2628-0.01320.03210.0241-0.05840.0167-0.0018-0.03290.0626-0.00350.0284-0.01730.01140.0526-0.01860.051226.034665.978458.5027
40.41260.1897-0.32860.3461-0.19750.70580.0413-0.02940.03480.0498-0.0043-0.0237-0.12080.0091-0.03690.03830.0012-0.00490.00870.00920.071-4.337315.5239100.0521
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 756
2X-RAY DIFFRACTION2B20 - 756
3X-RAY DIFFRACTION3C20 - 756
4X-RAY DIFFRACTION4D20 - 756

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