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- PDB-4ayo: Structure of The GH47 processing alpha-1,2-mannosidase from Caulo... -

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Basic information

Entry
Database: PDB / ID: 4ayo
TitleStructure of The GH47 processing alpha-1,2-mannosidase from Caulobacter strain K31
ComponentsMANNOSYL-OLIGOSACCHARIDE 1,2-ALPHA-MANNOSIDASE
KeywordsHYDROLASE / ALPHA-MANNOSIDASE / GLYCOSIDE HYDROLASE / GH47 / CAZY / ENZYME-CARBOHYDRATE INTERACTION GLYCOSIDASE INHIBITION
Function / homology
Function and homology information


mannosyl-oligosaccharide 1,2-alpha-mannosidase / mannosyl-oligosaccharide 1,2-alpha-mannosidase activity / endoplasmic reticulum mannose trimming / carbohydrate metabolic process / calcium ion binding / membrane
Similarity search - Function
ER degradation-enhancing alpha-mannosidase-like protein 1/2/3 / Glycoside hydrolase family 47 / Seven-hairpin glycosidases / Glycosyl hydrolase family 47 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Glycosyltransferase / Alpha/alpha barrel / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Mainly Alpha
Similarity search - Domain/homology
Mannosyl-oligosaccharide 1,2-alpha-mannosidase
Similarity search - Component
Biological speciesCAULOBACTER SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.85 Å
AuthorsThompson, A.J. / Dabin, J. / Iglesias-Fernandez, J. / Iglesias-Fernandez, A. / Dinev, Z. / Williams, S.J. / Siriwardena, A. / Moreland, C. / Hu, T.C. / Smith, D.K. ...Thompson, A.J. / Dabin, J. / Iglesias-Fernandez, J. / Iglesias-Fernandez, A. / Dinev, Z. / Williams, S.J. / Siriwardena, A. / Moreland, C. / Hu, T.C. / Smith, D.K. / Gilbert, H.J. / Rovira, C. / Davies, G.J.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2012
Title: The Reaction Coordinate of a Bacterial Gh47 Alpha-Mannosidase: A Combined Quantum Mechanical and Structural Approach.
Authors: Thompson, A.J. / Dabin, J. / Iglesias-Fernandez, J. / Ardevol, A. / Dinev, Z. / Williams, S.J. / Bande, O. / Siriwardena, A. / Moreland, C. / Hu, T.C. / Smith, D.K. / Gilbert, H.J. / Rovira, C. / Davies, G.J.
History
DepositionJun 21, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2Dec 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_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_alt_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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_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: MANNOSYL-OLIGOSACCHARIDE 1,2-ALPHA-MANNOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8595
Polymers50,5471
Non-polymers3124
Water14,718817
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)143.770, 143.770, 50.155
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein MANNOSYL-OLIGOSACCHARIDE 1,2-ALPHA-MANNOSIDASE / ALPHA-1\ / 2-MANNOSIDASE


Mass: 50546.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAULOBACTER SP. (bacteria) / Strain: K31 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): TUNER
References: UniProt: B0SWV2, mannosyl-oligosaccharide 1,2-alpha-mannosidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 817 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL SEQUENCE TRUNCATION TO REMOVE SIGNAL PEPTIDE

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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: 1.98 Å3/Da / Density % sol: 38 % / Description: NONE
Crystal growpH: 6.5
Details: 0.2 M AMMONIUM ACETATE, 0.1 M BIS-TRIS PH 6.5, 22% WT/VOL PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.8
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2011 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 0.85→46.52 Å / Num. obs: 312602 / % possible obs: 91.9 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.9
Reflection shellResolution: 0.85→0.9 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.6 / % possible all: 63.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0025refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NXC

1nxc


Resolution: 0.85→46.57 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.985 / SU B: 0.207 / SU ML: 0.006 / Cross valid method: THROUGHOUT / ESU R: 0.011 / ESU R Free: 0.011 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.10478 15793 5.1 %RANDOM
Rwork0.09464 ---
obs0.09515 296806 91.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.363 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 0.85→46.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3451 0 17 817 4285
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023705
X-RAY DIFFRACTIONr_bond_other_d0.0010.023438
X-RAY DIFFRACTIONr_angle_refined_deg1.4041.9485062
X-RAY DIFFRACTIONr_angle_other_deg0.78637903
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1445474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.95222.951183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.39315593
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8511533
X-RAY DIFFRACTIONr_chiral_restr0.0850.2534
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214274
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02925
X-RAY DIFFRACTIONr_nbd_refined0.2580.21948
X-RAY DIFFRACTIONr_nbd_other0.1680.23376
X-RAY DIFFRACTIONr_nbtor_refined0.1880.21803
X-RAY DIFFRACTIONr_nbtor_other0.0850.21787
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2116
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0760.23
X-RAY DIFFRACTIONr_metal_ion_refined0.0710.29
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3110.2223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.160.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.9730.23
X-RAY DIFFRACTIONr_symmetry_hbond_other0.3380.22
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.62137143
X-RAY DIFFRACTIONr_sphericity_free28.7125123
X-RAY DIFFRACTIONr_sphericity_bonded5.50157777
LS refinement shellResolution: 0.85→0.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 671 -
Rwork0.233 13510 -
obs--56.29 %

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