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- PDB-6b9p: Structure of GH 38 Jack Bean alpha-mannosidase in complex with a ... -

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Basic information

Entry
Database: PDB / ID: 6b9p
TitleStructure of GH 38 Jack Bean alpha-mannosidase in complex with a 36-valent iminosugar cluster inhibitor
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
Chem-D0J / Alpha-mannosidase
Similarity search - Component
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.996 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_unobs_or_zero_occ_atoms / 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.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.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)228,32310
Polymers222,4512
Non-polymers5,8728
Water24,6271367
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14000 Å2
ΔGint105 kcal/mol
Surface area62180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.274, 119.761, 277.050
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

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Protein , 1 types, 2 molecules AB

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


Mass: 111225.609 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: C0HJB3*PLUS, alpha-mannosidase

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Sugars , 2 types, 4 molecules

#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

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Non-polymers , 3 types, 1371 molecules

#4: Chemical ChemComp-D0J / (2R,3R,4R,5S)-2-(hydroxymethyl)-1-{9-[4-(methoxymethyl)-1H-1,2,3-triazol-1-yl]nonyl}piperidine-3,4,5-triol


Mass: 400.513 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H36N4O5
#5: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 1367 / 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: 2.63 Å3/Da / Density % sol: 53.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2M Potassium Sodium tartrate, 10% PEG 1500

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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: 1.996→48.26 Å / Num. obs: 291174 / % possible obs: 99 % / Redundancy: 7.03 % / CC1/2: 0.788 / Rrim(I) all: 0.167 / Net I/σ(I): 10.8
Reflection shellResolution: 1.996→2.12 Å / Redundancy: 7.03 % / Num. unique obs: 45423 / CC1/2: 0.753 / % possible all: 95.5

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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: 1.996→48.258 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.26 / Phase error: 22.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2254 14622 5.02 %
Rwork0.178 --
obs0.1804 291165 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.996→48.258 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14928 0 390 1367 16685
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00915766
X-RAY DIFFRACTIONf_angle_d0.99721424
X-RAY DIFFRACTIONf_dihedral_angle_d4.24412925
X-RAY DIFFRACTIONf_chiral_restr0.0562366
X-RAY DIFFRACTIONf_plane_restr0.0062711
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9961-2.01870.35583960.33647640X-RAY DIFFRACTION82
2.0187-2.04250.32594830.28969175X-RAY DIFFRACTION98
2.0425-2.06740.31894880.27189232X-RAY DIFFRACTION100
2.0674-2.09360.29244940.25159310X-RAY DIFFRACTION99
2.0936-2.12110.3094840.25849157X-RAY DIFFRACTION99
2.1211-2.15020.2834870.24619301X-RAY DIFFRACTION100
2.1502-2.18090.27914990.23089241X-RAY DIFFRACTION99
2.1809-2.21340.28164890.22919236X-RAY DIFFRACTION100
2.2134-2.2480.26784890.21859282X-RAY DIFFRACTION99
2.248-2.28490.26994890.22019245X-RAY DIFFRACTION100
2.2849-2.32430.26514800.21469250X-RAY DIFFRACTION99
2.3243-2.36650.24844930.20439276X-RAY DIFFRACTION100
2.3665-2.41210.25484880.20199291X-RAY DIFFRACTION99
2.4121-2.46130.25564860.2049195X-RAY DIFFRACTION100
2.4613-2.51480.25254880.19519239X-RAY DIFFRACTION99
2.5148-2.57330.24374980.19469370X-RAY DIFFRACTION100
2.5733-2.63770.26094910.19489224X-RAY DIFFRACTION100
2.6377-2.7090.24974900.19439285X-RAY DIFFRACTION100
2.709-2.78870.25244950.18479338X-RAY DIFFRACTION100
2.7887-2.87870.24374850.17689242X-RAY DIFFRACTION100
2.8787-2.98150.22424880.17889325X-RAY DIFFRACTION100
2.9815-3.10090.23064830.17539306X-RAY DIFFRACTION100
3.1009-3.2420.23594940.17169297X-RAY DIFFRACTION100
3.242-3.41290.22064980.16669265X-RAY DIFFRACTION100
3.4129-3.62660.21314870.15799327X-RAY DIFFRACTION100
3.6266-3.90660.19534970.14799313X-RAY DIFFRACTION100
3.9066-4.29950.164910.13149302X-RAY DIFFRACTION100
4.2995-4.92110.16364870.12379277X-RAY DIFFRACTION100
4.9211-6.1980.17385050.14099334X-RAY DIFFRACTION100
6.198-48.27170.1945000.16299268X-RAY DIFFRACTION100

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