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- PDB-6b9o: Structure of GH 38 Jack Bean alpha-mannosidase -

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Basic information

Entry
Database: PDB / ID: 6b9o
TitleStructure of GH 38 Jack Bean alpha-mannosidase
ComponentsAlpha-mannosidase from Canavalia ensiformis (jack bean)
KeywordsHYDROLASE / Mannosidase / PLANT PROTEIN
Function / homology
Function and homology information


alpha-mannosidase / protein storage vacuole / alpha-mannosidase activity / mannose metabolic process / carbohydrate binding / metal ion binding
Similarity search - Function
Glycosyl hydrolases family 38, C-terminal beta sandwich domain / Glycosyl hydrolases family 38 C-terminal beta sandwich domain / : / Glycoside hydrolase family 38, N-terminal domain / Glycosyl hydrolase family 38, C-terminal / Glycoside hydrolase family 38, central domain / Glycoside hydrolase family 38, central domain superfamily / Glycosyl hydrolases family 38 N-terminal domain / Glycosyl hydrolases family 38 C-terminal domain / Alpha mannosidase middle domain ...Glycosyl hydrolases family 38, C-terminal beta sandwich domain / Glycosyl hydrolases family 38 C-terminal beta sandwich domain / : / Glycoside hydrolase family 38, N-terminal domain / Glycosyl hydrolase family 38, C-terminal / Glycoside hydrolase family 38, central domain / Glycoside hydrolase family 38, central domain superfamily / Glycosyl hydrolases family 38 N-terminal domain / Glycosyl hydrolases family 38 C-terminal domain / Alpha mannosidase middle domain / Alpha mannosidase, middle domain / Glycoside hydrolase 38, N-terminal domain superfamily / Glycoside hydrolase families 57/38, central domain superfamily / Glycoside hydrolase/deacetylase, beta/alpha-barrel / Galactose mutarotase-like domain superfamily / Glycosyl hydrolase, all-beta
Similarity search - Domain/homology
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.841 Å
AuthorsHoward, E. / Cousido-Siah, A. / Lepage, M. / Bodlenner, A. / Mitschler, A. / Meli, A. / De Riccardis, F. / Izzo, I. / Podjarny, A. / Compain, P.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: Structural Basis of Outstanding Multivalent Effects in Jack Bean alpha-Mannosidase Inhibition.
Authors: Howard, E. / Cousido-Siah, A. / Lepage, M.L. / Schneider, J.P. / Bodlenner, A. / Mitschler, A. / Meli, A. / Izzo, I. / Alvarez, H.A. / Podjarny, A. / Compain, P.
History
DepositionOct 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / 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_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.pdbx_role / _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_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-mannosidase from Canavalia ensiformis (jack bean)
B: Alpha-mannosidase from Canavalia ensiformis (jack bean)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,5548
Polymers222,4832
Non-polymers5,0716
Water32,9311828
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13940 Å2
ΔGint18 kcal/mol
Surface area62890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.305, 119.667, 277.689
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Alpha-mannosidase from Canavalia ensiformis (jack bean)


Mass: 111241.609 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: C0HJB3*PLUS, alpha-mannosidase
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 2045.809 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-3[DManpa1-2DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,12,11/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-h1_d2-e1_e2-f1_f3-g1_h3-i1_h6-k1_i2-j1_k2-l1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1828 / 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: 2.62 Å3/Da / Density % sol: 53.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2M tri-ammonium citrate, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.92019 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92019 Å / Relative weight: 1
ReflectionResolution: 1.84→49.55 Å / Num. obs: 193407 / % possible obs: 99.2 % / Redundancy: 6.55 % / Biso Wilson estimate: 23.3300647617 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.177 / Net I/σ(I): 10.79
Reflection shellResolution: 1.84→1.95 Å / Redundancy: 5.96 % / Mean I/σ(I) obs: 1.28 / Num. unique obs: 57728 / CC1/2: 0.486 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O7D

1o7d


Resolution: 1.841→49.55 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2164 9670 5 %
Rwork0.1751 --
obs0.1771 193407 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.841→49.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15022 0 334 1829 17185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815902
X-RAY DIFFRACTIONf_angle_d1.03221634
X-RAY DIFFRACTIONf_dihedral_angle_d5.16213038
X-RAY DIFFRACTIONf_chiral_restr0.0582386
X-RAY DIFFRACTIONf_plane_restr0.0062750
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8409-1.86180.33212620.32674977X-RAY DIFFRACTION82
1.8618-1.88370.33763210.28726094X-RAY DIFFRACTION100
1.8837-1.90670.29513210.26366100X-RAY DIFFRACTION100
1.9067-1.93090.27853220.25276114X-RAY DIFFRACTION100
1.9309-1.95630.29883200.24446092X-RAY DIFFRACTION100
1.9563-1.98310.27343220.23816111X-RAY DIFFRACTION100
1.9831-2.01140.28343200.22946073X-RAY DIFFRACTION100
2.0114-2.04140.27423230.22496133X-RAY DIFFRACTION100
2.0414-2.07330.25513180.21856064X-RAY DIFFRACTION100
2.0733-2.10730.26183240.20336160X-RAY DIFFRACTION100
2.1073-2.14360.26563210.19716088X-RAY DIFFRACTION100
2.1436-2.18260.23133220.18846114X-RAY DIFFRACTION100
2.1826-2.22460.22233210.18476101X-RAY DIFFRACTION100
2.2246-2.270.23163230.18526130X-RAY DIFFRACTION100
2.27-2.31940.23143240.17796154X-RAY DIFFRACTION100
2.3194-2.37330.23433210.17876104X-RAY DIFFRACTION100
2.3733-2.43270.22393220.17476125X-RAY DIFFRACTION100
2.4327-2.49840.22713270.17576206X-RAY DIFFRACTION100
2.4984-2.5720.22623200.17726087X-RAY DIFFRACTION100
2.572-2.6550.23053230.17396146X-RAY DIFFRACTION100
2.655-2.74990.21233230.17196152X-RAY DIFFRACTION100
2.7499-2.85990.2073260.17426194X-RAY DIFFRACTION100
2.8599-2.99010.25363240.17956144X-RAY DIFFRACTION100
2.9901-3.14770.22413250.17326195X-RAY DIFFRACTION100
3.1477-3.34490.19673280.16896233X-RAY DIFFRACTION100
3.3449-3.60310.19393260.15976200X-RAY DIFFRACTION100
3.6031-3.96550.18233290.14586242X-RAY DIFFRACTION100
3.9655-4.5390.16043300.12946278X-RAY DIFFRACTION100
4.539-5.71730.16543340.13566345X-RAY DIFFRACTION100
5.7173-49.56790.20043480.16736581X-RAY DIFFRACTION100

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