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- PDB-7fe2: Crystal structure of the mutant E494Q of GH92 alpha-1,2-mannosida... -

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Basic information

Entry
Database: PDB / ID: 7fe2
TitleCrystal structure of the mutant E494Q of GH92 alpha-1,2-mannosidase from Enterococcus faecalis ATCC 10100 in complex with alpha-1,2-mannobiose
ComponentsAlpha-1,2-mannosidase
KeywordsHYDROLASE / Glycoside hydrolase / GH92 / Inhibitor / Carbohydrate / N-glycan
Function / homologyACETATE ION / :
Function and homology information
Biological speciesEnterococcus faecalis ATCC 10100 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMiyazaki, T. / Alonso-Gil, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19K15748 Japan
CitationJournal: Chemistry / Year: 2022
Title: Unlocking the Hydrolytic Mechanism of GH92 alpha-1,2-Mannosidases: Computation Inspires the use of C-Glycosides as Michaelis Complex Mimics.
Authors: Alonso-Gil, S. / Parkan, K. / Kaminsky, J. / Pohl, R. / Miyazaki, T.
History
DepositionJul 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 23, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-1,2-mannosidase
B: Alpha-1,2-mannosidase
C: Alpha-1,2-mannosidase
D: Alpha-1,2-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)334,28644
Polymers330,9324
Non-polymers3,35340
Water31,9411773
1
A: Alpha-1,2-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,69413
Polymers82,7331
Non-polymers96112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-1,2-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,57011
Polymers82,7331
Non-polymers83710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Alpha-1,2-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,51110
Polymers82,7331
Non-polymers7789
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Alpha-1,2-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,51110
Polymers82,7331
Non-polymers7789
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)162.626, 168.610, 260.282
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Alpha-1,2-mannosidase


Mass: 82733.078 Da / Num. of mol.: 4 / Mutation: E494Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis ATCC 10100 (bacteria)
Gene: WOW_02008 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A6N0WQ22
#2: Polysaccharide
alpha-D-mannopyranose-(1-2)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1122h-1b_1-5][a1122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(2+1)][a-D-Manp]{}}LINUCSPDB-CARE

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Non-polymers , 5 types, 1809 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1773 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.73 Å3/Da / Density % sol: 54.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium citrate, pH 5.0-5.6, 100 mM magnesium acetate, 200 mM ammonium sulfate, 5% PEG 20000
PH range: 5.0-5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Jun 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 354371 / % possible obs: 99.6 % / Redundancy: 13.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.04 / Rrim(I) all: 0.147 / Net I/σ(I): 12.2
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 12.8 % / Rmerge(I) obs: 1.254 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 51164 / CC1/2: 0.681 / Rpim(I) all: 0.361 / Rrim(I) all: 1.305 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DWO

6dwo


Resolution: 1.75→48.566 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.183 / WRfactor Rwork: 0.155 / SU B: 2.499 / SU ML: 0.076 / Average fsc free: 0.9176 / Average fsc work: 0.9269 / Cross valid method: FREE R-VALUE / ESU R: 0.098 / ESU R Free: 0.096
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1979 17508 4.942 %
Rwork0.1686 336788 -
all0.17 --
obs-354296 99.555 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 26 Å2
Baniso -1Baniso -2Baniso -3
1--0.506 Å2-0 Å20 Å2
2---0.339 Å2-0 Å2
3---0.845 Å2
Refinement stepCycle: LAST / Resolution: 1.75→48.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23052 0 212 1773 25037
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01323983
X-RAY DIFFRACTIONr_bond_other_d0.0010.01721452
X-RAY DIFFRACTIONr_angle_refined_deg1.6121.65532564
X-RAY DIFFRACTIONr_angle_other_deg1.4111.57549535
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.04352862
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.74124.0211318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.244153786
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8791576
X-RAY DIFFRACTIONr_chiral_restr0.0910.23030
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0227585
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025843
X-RAY DIFFRACTIONr_nbd_refined0.2030.24765
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.220654
X-RAY DIFFRACTIONr_nbtor_refined0.1760.211657
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.210796
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.21605
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0150.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0780.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1690.255
X-RAY DIFFRACTIONr_nbd_other0.1860.2286
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1160.263
X-RAY DIFFRACTIONr_mcbond_it2.0842.57311408
X-RAY DIFFRACTIONr_mcbond_other2.0842.57311407
X-RAY DIFFRACTIONr_mcangle_it2.9683.85214255
X-RAY DIFFRACTIONr_mcangle_other2.9683.85214256
X-RAY DIFFRACTIONr_scbond_it2.8542.84812575
X-RAY DIFFRACTIONr_scbond_other2.8542.84812576
X-RAY DIFFRACTIONr_scangle_it4.2954.15618300
X-RAY DIFFRACTIONr_scangle_other4.2954.15618301
X-RAY DIFFRACTIONr_lrange_it5.67530.59527439
X-RAY DIFFRACTIONr_lrange_other5.63230.35227084
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.7950.29512990.27624612X-RAY DIFFRACTION98.9574
1.795-1.8450.29112200.25724015X-RAY DIFFRACTION99.1007
1.845-1.8980.2712080.23823389X-RAY DIFFRACTION99.1615
1.898-1.9570.25312440.22822731X-RAY DIFFRACTION99.263
1.957-2.0210.25911780.21922046X-RAY DIFFRACTION99.3838
2.021-2.0920.2411150.20221408X-RAY DIFFRACTION99.4744
2.092-2.1710.22610890.18820646X-RAY DIFFRACTION99.4873
2.171-2.2590.2310310.18619910X-RAY DIFFRACTION99.6384
2.259-2.360.2159830.17419111X-RAY DIFFRACTION99.6825
2.36-2.4750.2179510.1718307X-RAY DIFFRACTION99.7307
2.475-2.6080.2068330.16517515X-RAY DIFFRACTION99.7879
2.608-2.7670.1888510.15316548X-RAY DIFFRACTION99.8909
2.767-2.9580.1917750.15515571X-RAY DIFFRACTION99.89
2.958-3.1940.1837410.15214516X-RAY DIFFRACTION99.9738
3.194-3.4990.1857150.15913351X-RAY DIFFRACTION99.9858
3.499-3.9120.1626630.14612114X-RAY DIFFRACTION99.9609
3.912-4.5160.1425680.12410735X-RAY DIFFRACTION99.9912
4.516-5.5290.1474730.1319092X-RAY DIFFRACTION99.9687
5.529-7.8130.1783590.1477155X-RAY DIFFRACTION100
7.813-48.5660.1752120.1644018X-RAY DIFFRACTION99.1097

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