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- PDB-8b5m: Crystal structure of GH47 alpha-1,2-mannosidase from Caulobacter ... -

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Basic information

Entry
Database: PDB / ID: 8b5m
TitleCrystal structure of GH47 alpha-1,2-mannosidase from Caulobacter K31 strain in complex with cyclosulfamidate inhibitor
ComponentsMannosyl-oligosaccharide 1,2-alpha-mannosidase
KeywordsHYDROLASE / Carbohydrate / Mannosidase / Inverting
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 / Six-hairpin glycosidase-like superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
Chem-5OV / Mannosyl-oligosaccharide 1,2-alpha-mannosidase
Similarity search - Component
Biological speciesCaulobacter (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.97 Å
AuthorsMales, A. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T004819/1 United Kingdom
CitationJournal: To Be Published
Title: GH47 and Cyclosulfamidate
Authors: Males, A. / Davies, G.J. / Artola, M. / Overkleeft, H.S.
History
DepositionSep 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release

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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)50,8795
Polymers50,5211
Non-polymers3584
Water12,376687
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.134, 144.134, 50.320
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Mannosyl-oligosaccharide 1,2-alpha-mannosidase


Mass: 50520.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter (bacteria) / Strain: K31 / Gene: Caul_4035 / Production host: Escherichia coli (E. coli)
References: UniProt: B0SWV2, mannosyl-oligosaccharide 1,2-alpha-mannosidase
#2: Chemical ChemComp-5OV / (3aR,4S,5S,6R,7R,7aS)-7-(hydroxymethyl)-2,2-bis(oxidanylidene)-3a,4,5,6,7,7a-hexahydro-3H-benzo[d][1,2,3]oxathiazole-4,5,6-triol / Cyclophellitol Sulfamidate probe KK131


Mass: 255.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H13NO7S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 687 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.06 Å3/Da / Density % sol: 40.17 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 23% PEG3350, 0.1 M MES pH 7.0, 0.2 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.799 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.799 Å / Relative weight: 1
ReflectionResolution: 0.97→72.07 Å / Num. obs: 230864 / % possible obs: 100 % / Redundancy: 10.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.05 / Net I/σ(I): 7.7
Reflection shellResolution: 0.97→0.99 Å / Redundancy: 10 % / Rmerge(I) obs: 1.49 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 11558 / CC1/2: 0.605 / Rpim(I) all: 0.49 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AYO

4ayo


Resolution: 0.97→72.067 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.309 / SU ML: 0.016 / Cross valid method: FREE R-VALUE / ESU R: 0.02 / ESU R Free: 0.02
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.148 11679 5.059 %
Rwork0.1373 219185 -
all0.138 --
obs-230864 99.987 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 7.642 Å2
Baniso -1Baniso -2Baniso -3
1--0.041 Å2-0.021 Å20 Å2
2---0.041 Å20 Å2
3---0.133 Å2
Refinement stepCycle: LAST / Resolution: 0.97→72.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3446 0 19 687 4152
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0133687
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153378
X-RAY DIFFRACTIONr_angle_refined_deg1.9191.6455045
X-RAY DIFFRACTIONr_angle_other_deg1.6981.587776
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4935472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.54321.256207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.65115579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5081529
X-RAY DIFFRACTIONr_chiral_restr0.1210.2470
X-RAY DIFFRACTIONr_chiral_restr_other0.0520.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024249
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02925
X-RAY DIFFRACTIONr_nbd_refined0.2330.2779
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.23299
X-RAY DIFFRACTIONr_nbtor_refined0.190.21798
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.21585
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2410
X-RAY DIFFRACTIONr_metal_ion_refined0.0740.211
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2260.29
X-RAY DIFFRACTIONr_nbd_other0.2270.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1820.263
X-RAY DIFFRACTIONr_mcbond_it0.7040.6141785
X-RAY DIFFRACTIONr_mcbond_other0.6980.6131784
X-RAY DIFFRACTIONr_mcangle_it1.0380.9262240
X-RAY DIFFRACTIONr_mcangle_other1.040.9272241
X-RAY DIFFRACTIONr_scbond_it1.2380.7351902
X-RAY DIFFRACTIONr_scbond_other1.2370.7351903
X-RAY DIFFRACTIONr_scangle_it1.7591.0632787
X-RAY DIFFRACTIONr_scangle_other1.7581.0632788
X-RAY DIFFRACTIONr_lrange_it3.2848.4874570
X-RAY DIFFRACTIONr_lrange_other2.6437.5024348
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
0.97-0.9950.268960.254161880.254170840.8460.8481000.259
0.995-1.0220.2338180.226158810.226166990.8920.891000.229
1.022-1.0520.2138170.207153790.207161960.9120.9121000.207
1.052-1.0840.1948140.186148650.187156790.930.9331000.184
1.084-1.120.1797720.17145010.17152730.9430.9451000.166
1.12-1.1590.1777740.16139240.161146980.9490.9531000.154
1.159-1.2030.1557030.149135340.149142370.960.9631000.142
1.203-1.2520.1616610.145130510.146137120.9590.9641000.137
1.252-1.3080.1496590.142124410.142131000.9660.9661000.134
1.308-1.3720.1376400.133119430.133125830.9710.9721000.125
1.372-1.4460.1425980.128112990.129118970.9710.9721000.12
1.446-1.5340.1325720.118107110.119112830.9750.9771000.111
1.534-1.6390.125630.111100290.111105920.980.9811000.104
1.639-1.7710.1245480.10993330.1198810.980.9821000.103
1.771-1.940.1284160.11586540.11590700.9790.9811000.109
1.94-2.1680.1224080.11177990.11182070.9810.9831000.106
2.168-2.5030.1113660.10668830.10672490.9840.9841000.102
2.503-3.0650.1072820.11458240.11461060.9840.9831000.111
3.065-4.3310.1492410.11844820.1247230.9730.9791000.115
4.331-72.0670.1741310.16124630.16125950.9750.97599.96150.161

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