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- PDB-6ddt: mouse beta-mannosidase (MANBA) -

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Basic information

Entry
Database: PDB / ID: 6ddt
Titlemouse beta-mannosidase (MANBA)
ComponentsBeta-mannosidase
KeywordsHYDROLASE / mannosidase lysosomal glycosidase GH2
Function / homology
Function and homology information


Lysosomal oligosaccharide catabolism / beta-mannosidase / beta-mannosidase activity / glycoprotein catabolic process / oligosaccharide catabolic process / mannose binding / Neutrophil degranulation / lysosomal lumen / lysosome / hydrolase activity / extracellular space
Similarity search - Function
Mannosidase Ig/CBM-like domain / Beta-mannosidase, Ig-fold domain / Ig-fold domain / Mannosidase Ig/CBM-like domain / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Beta-Galactosidase/glucuronidase domain superfamily / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily ...Mannosidase Ig/CBM-like domain / Beta-mannosidase, Ig-fold domain / Ig-fold domain / Mannosidase Ig/CBM-like domain / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Beta-Galactosidase/glucuronidase domain superfamily / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Alpha Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGytz, H. / Liang, J. / Liang, Y. / Gorelik, A. / Illes, K. / Nagar, B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-133535 Canada
CitationJournal: FEBS J. / Year: 2019
Title: The structure of mammalian beta-mannosidase provides insight into beta-mannosidosis and nystagmus.
Authors: Gytz, H. / Liang, J. / Liang, Y. / Gorelik, A. / Illes, K. / Nagar, B.
History
DepositionMay 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / struct_asym / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 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: Beta-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,37112
Polymers100,0561
Non-polymers2,31411
Water10,233568
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.584, 65.458, 104.414
Angle α, β, γ (deg.)90.00, 92.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-mannosidase / / Lysosomal beta A mannosidase / Mannanase / Mannase


Mass: 100056.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Manba, Bmn / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8K2I4, beta-mannosidase

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Sugars , 4 types, 6 molecules

#2: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}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.: 1
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: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 573 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 568 / 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: 2.75 Å3/Da / Density % sol: 55.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 19-21% PEG 5000, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→46.152 Å / Num. obs: 48793 / % possible obs: 76.6 % / Redundancy: 3.3 % / Net I/σ(I): 17.2
Reflection shellResolution: 2.1→2.18 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N6U

5n6u


Resolution: 2.1→46.152 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.13
RfactorNum. reflection% reflection
Rfree0.2059 1883 3.86 %
Rwork0.1738 --
obs0.1751 48793 76.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→46.152 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7015 0 149 568 7732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047381
X-RAY DIFFRACTIONf_angle_d0.63310042
X-RAY DIFFRACTIONf_dihedral_angle_d12.4814295
X-RAY DIFFRACTIONf_chiral_restr0.0451092
X-RAY DIFFRACTIONf_plane_restr0.0031262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1003-2.15710.2633600.23461381X-RAY DIFFRACTION30
2.1571-2.22060.2921750.221919X-RAY DIFFRACTION41
2.2206-2.29230.1917960.21712342X-RAY DIFFRACTION50
2.2923-2.37420.23971130.21212694X-RAY DIFFRACTION58
2.3742-2.46920.26951260.20793097X-RAY DIFFRACTION67
2.4692-2.58160.24341390.20753545X-RAY DIFFRACTION75
2.5816-2.71770.23081650.20364055X-RAY DIFFRACTION87
2.7177-2.8880.23211760.19924466X-RAY DIFFRACTION94
2.888-3.11090.25181810.19064530X-RAY DIFFRACTION97
3.1109-3.42390.22921780.17164626X-RAY DIFFRACTION98
3.4239-3.91910.16961890.15134672X-RAY DIFFRACTION99
3.9191-4.93670.16181970.12894744X-RAY DIFFRACTION100
4.9367-46.16320.19071880.17384839X-RAY DIFFRACTION100
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)
10.80580.21630.03190.7570.14721.0356-0.0340.14340.0209-0.05250.0712-0.2357-0.33240.1765-0.01660.2357-0.02360.02140.12710.00340.173237.450962.2518121.8304
21.09290.1509-0.07771.31090.78930.95440.0008-0.22750.1770.2383-0.14910.0557-0.32310.0270.01770.8882-0.0706-0.03870.111-0.06230.263125.476476.118150.3216
30.81750.24570.26120.61220.29680.58460.0119-0.09450.17510.3535-0.13690.239-0.2652-0.3831-0.00260.4919-0.03720.1180.2968-0.07180.228713.482764.6622147.8159
40.79280.0911-0.09130.98880.18291.450.058-0.0288-0.10870.3174-0.08250.04480.2516-0.24050.03260.2377-0.0447-0.00970.1033-0.00690.151423.3947.3765138.4616
50.3630.08-0.2570.3544-0.2550.40160.00690.1826-0.2929-0.019-0.22330.14040.5899-0.57130.02230.3591-0.20970.030.4148-0.13790.311713.068134.334116.7236
60.30230.0108-0.2840.1497-0.12320.4820.1270.196-0.25350.2504-0.33660.47980.578-1.0996-0.00170.3422-0.53930.21390.9128-0.23580.5736-2.932135.8303132.8383
70.41310.12960.03080.45560.25440.3865-0.0190.3283-0.0581-0.1511-0.17020.51110.0215-0.7992-0.06740.1944-0.1063-0.16320.9926-0.14390.5113-3.905646.2701113.6496
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 212 )
2X-RAY DIFFRACTION2chain 'A' and (resid 213 through 280 )
3X-RAY DIFFRACTION3chain 'A' and (resid 281 through 341 )
4X-RAY DIFFRACTION4chain 'A' and (resid 342 through 562 )
5X-RAY DIFFRACTION5chain 'A' and (resid 563 through 640 )
6X-RAY DIFFRACTION6chain 'A' and (resid 641 through 804 )
7X-RAY DIFFRACTION7chain 'A' and (resid 805 through 879 )

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