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- PDB-2ww0: Structure of the Family GH92 Inverting Mannosidase BT3990 from Ba... -

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Basic information

Entry
Database: PDB / ID: 2ww0
TitleStructure of the Family GH92 Inverting Mannosidase BT3990 from Bacteroides thetaiotaomicron VPI-5482
ComponentsPUTATIVE ALPHA-1,2-MANNOSIDASE
KeywordsHYDROLASE / GH92 / BT3990 / GLYCOSIDE HYDROLASE FAMILY 92
Function / homology
Function and homology information


peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity / glycoprotein catabolic process / protein quality control for misfolded or incompletely synthesized proteins / 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
1S-8AB-OCTAHYDRO-INDOLIZIDINE-1A,2A,8B-TRIOL / Alpha-1,2-mannosidase
Similarity search - Component
Biological speciesBACTEROIDES THETAIOTAOMICRON (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSuits, M.D.L. / Thompson, A. / Zhu, Y. / 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 1.2May 22, 2013Group: Derived calculations / Non-polymer description / Refinement description
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_label_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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)688,79941
Polymers685,5278
Non-polymers3,27233
Water9,764542
1
A: PUTATIVE ALPHA-1,2-MANNOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3658
Polymers85,6911
Non-polymers6747
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)86,1806
Polymers85,6911
Non-polymers4905
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)86,1806
Polymers85,6911
Non-polymers4905
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)86,1806
Polymers85,6911
Non-polymers4905
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: PUTATIVE ALPHA-1,2-MANNOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0885
Polymers85,6911
Non-polymers3974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: PUTATIVE ALPHA-1,2-MANNOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,9964
Polymers85,6911
Non-polymers3053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: PUTATIVE ALPHA-1,2-MANNOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,9043
Polymers85,6911
Non-polymers2132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: PUTATIVE ALPHA-1,2-MANNOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,9043
Polymers85,6911
Non-polymers2132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.810, 151.960, 218.619
Angle α, β, γ (deg.)90.00, 93.43, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TRP / Beg label comp-ID: TRP / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 3 / Auth seq-ID: 22 - 753 / Label seq-ID: 3 - 734

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH

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Components

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


Mass: 85690.859 Da / Num. of mol.: 8 / Fragment: RESIDUES 20-755
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria)
Strain: VPI-5482 / Plasmid: PET 21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8A0N1
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SWA / 1S-8AB-OCTAHYDRO-INDOLIZIDINE-1A,2A,8B-TRIOL / SWAINSONINE / Swainsonine


Mass: 173.210 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H15NO3 / Comment: chemotherapy, inhibitor, alkaloid*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 542 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details1S-8AB-OCTAHYDRO-INDOLIZIDINE-1A,2A,8B-TRIOL (SWA): SWAINSONINE
Sequence detailsFIRST 19 RESIDUES WERE NOT INCLUDED IN RECOMBINANT PROTEIN USED

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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: 2.63 Å3/Da / Density % sol: 53.2 % / Description: NONE
Crystal growDetails: 20% W/V 6000 PEG, 0.2 M NH4CL, TRIS(HYDROXYMETHYL)AMINOMETHANE (PH 8.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 7, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.8→65.6 Å / Num. obs: 169366 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 53.4 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.7
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.9 / % possible all: 95.2

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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: 2.8→218.23 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.928 / SU B: 30.595 / SU ML: 0.256 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.21156 8505 5 %RANDOM
Rwork0.18439 ---
obs0.18577 160835 97.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.646 Å2
Baniso -1Baniso -2Baniso -3
1--3.12 Å20 Å2-2.78 Å2
2---2.25 Å20 Å2
3---5.04 Å2
Refinement stepCycle: LAST / Resolution: 2.8→218.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47598 0 206 542 48346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02249329
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2541.93766958
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.13455912
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.24924.4152537
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.082157803
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.56615205
X-RAY DIFFRACTIONr_chiral_restr0.0810.26740
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02138894
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_it0.2941.529324
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.61247270
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.028320005
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.7424.519673
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
1A2919tight positional0.040.05
2B2919tight positional0.040.05
3C2919tight positional0.040.05
4D2919tight positional0.040.05
5E2919tight positional0.040.05
6F2919tight positional0.040.05
7G2919tight positional0.040.05
8H2919tight positional0.040.05
1A2869loose positional0.055
2B2869loose positional0.065
3C2869loose positional0.055
4D2869loose positional0.065
5E2869loose positional0.055
6F2869loose positional0.055
7G2869loose positional0.065
8H2869loose positional0.085
1A2919tight thermal0.070.5
2B2919tight thermal0.070.5
3C2919tight thermal0.070.5
4D2919tight thermal0.070.5
5E2919tight thermal0.060.5
6F2919tight thermal0.060.5
7G2919tight thermal0.040.5
8H2919tight thermal0.040.5
1A2869loose thermal0.0910
2B2869loose thermal0.0810
3C2869loose thermal0.0810
4D2869loose thermal0.0810
5E2869loose thermal0.0710
6F2869loose thermal0.0610
7G2869loose thermal0.0510
8H2869loose thermal0.0610
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 588 -
Rwork0.288 11561 -
obs--95.1 %
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)
11.11940.03220.28890.73560.16450.4586-0.04880.0269-0.04530.03510.0805-0.10940.02840.0079-0.03170.13650.02910.02410.1576-0.07540.090341.01218.338108.179
21.02260.16920.06350.57040.07240.5085-0.09880.00180.1754-0.07720.04180.1090.0005-0.16530.0570.1252-0.0098-0.03240.2172-0.04190.10584.19344.628101.666
31.26040.04170.15130.8235-0.12260.4739-0.05510.10420.3129-0.01120.01110.1451-0.0375-0.09250.0440.16040.01150.0040.10260.02310.24158.9280.23258.485
41.6045-0.37350.2740.6979-0.02980.57660.15690.15010.0197-0.1577-0.1017-0.07660.05720.0796-0.05520.15440.01890.01540.08870.03770.0875-11.532-25.7954.386
51.38450.17610.12021.2267-0.30890.4768-0.08970.18010.314-0.36880.14480.33640.0855-0.0153-0.05510.2703-0.063-0.11770.13480.1220.26163.06650.18957.389
61.1743-0.3171-0.04082.3927-0.31210.452-0.00750.010.1779-0.4677-0.069-0.70040.11450.1510.07650.25710.01320.15130.20230.09030.507640.19176.35552.298
71.643-0.15270.64652.0851-0.31941.1966-0.152-0.01270.05250.29050.2004-0.53790.2809-0.0414-0.04840.8561-0.0435-0.32270.3367-0.09770.435847.86719.199-1.876
81.59760.41180.51751.53390.15651.0862-0.1692-0.32780.62810.36590.0910.7026-0.0065-0.57970.07820.6271-0.0789-0.10580.72250.03540.734211.08745.412-8.914
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 755
2X-RAY DIFFRACTION2B20 - 755
3X-RAY DIFFRACTION3C20 - 756
4X-RAY DIFFRACTION4D20 - 757
5X-RAY DIFFRACTION5E20 - 755
6X-RAY DIFFRACTION6F20 - 755
7X-RAY DIFFRACTION7G20 - 755
8X-RAY DIFFRACTION8H20 - 755

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