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- PDB-1nxc: Structure of mouse Golgi alpha-1,2-mannosidase IA reveals the mol... -

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Basic information

Entry
Database: PDB / ID: 1nxc
TitleStructure of mouse Golgi alpha-1,2-mannosidase IA reveals the molecular basis for substrate specificity among Class I enzymes (family 47 glycosidases)
ComponentsMannosyl-oligosaccharide 1,2-alpha-mannosidase IA
KeywordsHYDROLASE / mannosidase / glycosidase / Structural Genomics / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG
Function / homology
Function and homology information


Progressive trimming of alpha-1,2-linked mannose residues from Man9/8/7GlcNAc2 to produce Man5GlcNAc2 / mannosyl-oligosaccharide 1,2-alpha-mannosidase / mannosyl-oligosaccharide 1,2-alpha-mannosidase activity / protein targeting to ER / protein glycosylation / endoplasmic reticulum-Golgi intermediate compartment / : / cytoplasmic vesicle / carbohydrate metabolic process / Golgi membrane ...Progressive trimming of alpha-1,2-linked mannose residues from Man9/8/7GlcNAc2 to produce Man5GlcNAc2 / mannosyl-oligosaccharide 1,2-alpha-mannosidase / mannosyl-oligosaccharide 1,2-alpha-mannosidase activity / protein targeting to ER / protein glycosylation / endoplasmic reticulum-Golgi intermediate compartment / : / cytoplasmic vesicle / carbohydrate metabolic process / Golgi membrane / calcium ion binding / Golgi apparatus / endoplasmic reticulum / cytosol
Similarity search - Function
Glycoside hydrolase family 47 / Seven-hairpin glycosidases / Glycosyl hydrolase family 47 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
Mannosyl-oligosaccharide 1,2-alpha-mannosidase IA
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsTempel, W. / Liu, Z.-J. / Karaveg, K. / Rose, J. / Moremen, K.W. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structure of mouse Golgi alpha-mannosidase IA reveals the molecular basis for substrate specificity among class 1 (family 47 glycosylhydrolase) alpha1,2-mannosidases
Authors: Tempel, W. / Karaveg, K. / Liu, Z.-J. / Rose, J. / Wang, B.-C. / Moremen, K.W.
History
DepositionFeb 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
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.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mannosyl-oligosaccharide 1,2-alpha-mannosidase IA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9773
Polymers54,5401
Non-polymers1,4372
Water5,801322
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.288, 72.164, 129.571
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Mannosyl-oligosaccharide 1,2-alpha-mannosidase IA / Processing alpha-1 / 2-mannosidase IA / Alpha-1 / 2-mannosidase IA / Mannosidase alpha class 1A ...Processing alpha-1 / 2-mannosidase IA / Alpha-1 / 2-mannosidase IA / Mannosidase alpha class 1A member 1 / Man(9)-alpha-mannosidase


Mass: 54540.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: man1a / Plasmid: pHIL S1 / Production host: Pichia pastoris (fungus) / Strain (production host): GS115
References: UniProt: P45700, mannosyl-oligosaccharide 1,2-alpha-mannosidase
#2: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[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: 1397.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d6-e1_f3-g1_f6-h1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.25 Å3/Da / Density % sol: 44.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: PEG4000, pH 4.5-6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 22, 2002 / Details: MSC Blue Confocal Optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.51→62.5 Å / Num. all: 81971 / Num. obs: 73142 / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rsym value: 0.06 / Net I/σ(I): 10.2
Reflection shellResolution: 1.51→1.63 Å / Mean I/σ(I) obs: 3 / Rsym value: 0.147

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Processing

Software
NameVersionClassification
EPMRphasing
REFMAC5.1.24refinement
PROTEUM PLUS(BRUKER)data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→62.5 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.325 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1897 3689 5 %RANDOM
Rwork0.17079 ---
obs0.17174 69386 89.18 %-
all-82108 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 8.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2---0.39 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.51→62.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3693 0 95 322 4110
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213902
X-RAY DIFFRACTIONr_bond_other_d0.0020.023440
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.9675304
X-RAY DIFFRACTIONr_angle_other_deg0.90337952
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8375466
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0830.2580
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024263
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02825
X-RAY DIFFRACTIONr_nbd_refined0.220.2914
X-RAY DIFFRACTIONr_nbd_other0.2340.23762
X-RAY DIFFRACTIONr_nbtor_other0.1120.22331
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2186
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2260.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.6131.52313
X-RAY DIFFRACTIONr_mcangle_it1.10423692
X-RAY DIFFRACTIONr_scbond_it1.66431589
X-RAY DIFFRACTIONr_scangle_it2.5874.51612
X-RAY DIFFRACTIONr_rigid_bond_restr1.33423871
X-RAY DIFFRACTIONr_sphericity_free5.322314
X-RAY DIFFRACTIONr_sphericity_bonded3.06923758
LS refinement shellResolution: 1.511→1.55 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.322 19
Rwork0.282 496

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