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

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Basic information

Entry
Database: PDB / ID: 4ayq
TitleStructure of The GH47 processing alpha-1,2-mannosidase from Caulobacter strain K31 in complex with mannoimidazole
ComponentsMANNOSYL-OLIGOSACCHARIDE 1,2-ALPHA-MANNOSIDASE
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / GH47 / CAZY / ENZYME-CARBOHYDRATE INTERACTION / MANNOSE / GLYCOSIDASE INHIBITION / QUANTUM MECHANICS
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
Chem-MVL / DI(HYDROXYETHYL)ETHER / Mannosyl-oligosaccharide 1,2-alpha-mannosidase
Similarity search - Component
Biological speciesCAULOBACTER SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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 1.2May 1, 2024Group: 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_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_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.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)51,38110
Polymers50,5471
Non-polymers8349
Water14,898827
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)143.607, 143.607, 50.026
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 836 molecules

#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-MVL / (5R,6R,7S,8R)-5-(HYDROXYMETHYL)-5,6,7,8-TETRAHYDROIMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL / Mannoimidazole


Mass: 200.192 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H12N2O4
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 827 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsN-TERMINAL 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: 1.97 Å3/Da / Density % sol: 37.8 % / Description: NONE
Crystal growpH: 6.5
Details: 0.2 M AMMONIUM ACTETATE, 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: I04 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 12, 2012 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.1→46.41 Å / Num. obs: 154906 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.7
Reflection shellResolution: 1.1→1.16 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 5.4 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.7.0025refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PREVIOUSLY SOLVED NATIVE STRUCTURE

Resolution: 1.1→41.49 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.983 / SU B: 0.5 / SU ML: 0.011 / Cross valid method: THROUGHOUT / ESU R: 0.02 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.10524 7772 5 %RANDOM
Rwork0.08848 ---
obs0.08932 147134 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.403 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.1→41.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3451 0 50 827 4328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023715
X-RAY DIFFRACTIONr_bond_other_d0.0010.023457
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.9495063
X-RAY DIFFRACTIONr_angle_other_deg0.81837943
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1235473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.88922.857182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.61515592
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.491533
X-RAY DIFFRACTIONr_chiral_restr0.0930.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214265
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02930
X-RAY DIFFRACTIONr_nbd_refined0.2730.21928
X-RAY DIFFRACTIONr_nbd_other0.1750.23525
X-RAY DIFFRACTIONr_nbtor_refined0.1930.21837
X-RAY DIFFRACTIONr_nbtor_other0.0860.21957
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.2113
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.10.21
X-RAY DIFFRACTIONr_metal_ion_refined0.070.211
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3060.2194
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2660.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
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_restr1.61437170
X-RAY DIFFRACTIONr_sphericity_free38.4565132
X-RAY DIFFRACTIONr_sphericity_bonded7.28157788
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.169 480 -
Rwork0.146 9814 -
obs--88.85 %

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