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- PDB-5ne5: Crystal structure of family 47 alpha-1,2-mannosidase from Cauloba... -

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Basic information

Entry
Database: PDB / ID: 5ne5
TitleCrystal structure of family 47 alpha-1,2-mannosidase from Caulobacter K31 strain in complex with kifunensine
ComponentsMannosyl-oligosaccharide 1,2-alpha-mannosidase
KeywordsHYDROLASE / Mannosidase Glycosidase Hydrolysis Inhibitor
Function / homology
Function and homology information


mannosyl-oligosaccharide 1,2-alpha-mannosidase / mannosyl-oligosaccharide 1,2-alpha-mannosidase activity / carbohydrate metabolic process / calcium ion binding / membrane
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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Mainly Alpha
Similarity search - Domain/homology
KIFUNENSINE / Mannosyl-oligosaccharide 1,2-alpha-mannosidase
Similarity search - Component
Biological speciesCaulobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.05 Å
AuthorsMales, A. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council United Kingdom
CitationJournal: Chembiochem / Year: 2017
Title: Conformational Analysis of the Mannosidase Inhibitor Kifunensine: A Quantum Mechanical and Structural Approach.
Authors: Males, A. / Raich, L. / Williams, S.J. / Rovira, C. / Davies, G.J.
History
DepositionMar 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2Aug 16, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,0916
Polymers50,5471
Non-polymers5455
Water7,530418
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-25 kcal/mol
Surface area14980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.923, 144.923, 50.593
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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


Mass: 50546.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter sp. (bacteria) / Strain: K31 / Gene: Caul_4035 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B0SWV2, mannosyl-oligosaccharide 1,2-alpha-mannosidase

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Non-polymers , 5 types, 423 molecules

#2: Chemical ChemComp-KIF / KIFUNENSINE


Mass: 232.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H12N2O6 / Comment: inhibitor, alkaloid*YM
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 2.6 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris pH 6.5, 0.2 M ammonium acetate, 22% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.05→36.23 Å / Num. obs: 183579 / % possible obs: 99.2 % / Redundancy: 4.7 % / CC1/2: 1 / Rmerge(I) obs: 0.09 / Net I/σ(I): 7
Reflection shellResolution: 1.05→1.07 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 9103 / CC1/2: 0.53 / % possible all: 99.6

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Processing

Software
NameVersionClassification
xia2data reduction
Aimlessdata scaling
REFMAC5.8.0158refinement
RefinementResolution: 1.05→36.23 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.979 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.025 / ESU R Free: 0.025
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1523 9277 5.1 %RANDOM
Rwork0.1456 ---
obs0.146 183575 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 85.85 Å2 / Biso mean: 11.7418 Å2 / Biso min: 5.73 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.05→36.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3427 0 33 418 3878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0193779
X-RAY DIFFRACTIONr_bond_other_d00.023432
X-RAY DIFFRACTIONr_angle_refined_deg1.8721.9485184
X-RAY DIFFRACTIONr_angle_other_deg3.67137957
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2755497
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.57423.016189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.02315616
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6681533
X-RAY DIFFRACTIONr_chiral_restr0.1190.2551
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024318
X-RAY DIFFRACTIONr_gen_planes_other0.020.02876
X-RAY DIFFRACTIONr_mcbond_it1.1660.9281795
X-RAY DIFFRACTIONr_mcbond_other1.1340.9261794
X-RAY DIFFRACTIONr_mcangle_it1.6311.4012259
LS refinement shellResolution: 1.05→1.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 708 -
Rwork0.25 12941 -
all-13649 -
obs--99.57 %

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