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- PDB-7fe1: Crystal structure of GH92 alpha-1,2-mannosidase from Enterococcus... -

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Basic information

Entry
Database: PDB / ID: 7fe1
TitleCrystal structure of GH92 alpha-1,2-mannosidase from Enterococcus faecalis ATCC 10100 in complex with methyl alpha-1,2-C-mannobioside
ComponentsAlpha-1,2-mannosidase
KeywordsHYDROLASE / Glycoside hydrolase / GH92 / Inhibitor / Carbohydrate / N-glycan
Function / homologymethyl 2-deoxy-2-methyl-alpha-D-mannopyranoside / ACETIC ACID / alpha-D-mannopyranose / :
Function and homology information
Biological speciesEnterococcus faecalis ATCC 10100 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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

Downloads & links

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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)333,91540
Polymers330,9364
Non-polymers2,97936
Water49,7212760
1
A: Alpha-1,2-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,54011
Polymers82,7341
Non-polymers80610
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-1,2-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,60212
Polymers82,7341
Non-polymers86811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Alpha-1,2-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4189
Polymers82,7341
Non-polymers6848
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Alpha-1,2-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3568
Polymers82,7341
Non-polymers6227
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)163.162, 169.601, 258.659
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 , 1 types, 4 molecules ABCD

#1: Protein
Alpha-1,2-mannosidase


Mass: 82734.070 Da / Num. of mol.: 4
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

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Sugars , 2 types, 8 molecules

#2: Sugar
ChemComp-5II / methyl 2-deoxy-2-methyl-alpha-D-mannopyranoside


Type: D-saccharide, alpha linking / Mass: 192.210 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H16O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 2788 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2760 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Nonpolymer detailsmethyl alpha-1,2-C-mannobioside is compounded from MAN and 5II.

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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: 2.7 Å3/Da / Density % sol: 54.5 %
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: Mar 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.72→50 Å / Num. obs: 375878 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.034 / Rrim(I) all: 0.125 / Net I/σ(I): 17.3
Reflection shellResolution: 1.72→1.81 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.168 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 54650 / CC1/2: 0.759 / Rpim(I) all: 0.327 / Rrim(I) all: 1.214 / % possible all: 100

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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: 1.72→48.621 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.872 / SU ML: 0.058 / Cross valid method: FREE R-VALUE / ESU R: 0.084 / ESU R Free: 0.081
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1714 18587 4.946 %
Rwork0.1489 357214 -
all0.15 --
obs-375801 99.99 %
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: 23.049 Å2
Baniso -1Baniso -2Baniso -3
1--0.029 Å2-0 Å20 Å2
2---0.022 Å2-0 Å2
3---0.051 Å2
Refinement stepCycle: LAST / Resolution: 1.72→48.621 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23052 0 184 2760 25996
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01323991
X-RAY DIFFRACTIONr_bond_other_d0.0010.01721449
X-RAY DIFFRACTIONr_angle_refined_deg1.7331.65432615
X-RAY DIFFRACTIONr_angle_other_deg1.4931.57649552
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.88952876
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.07923.9861317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.563153788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5151576
X-RAY DIFFRACTIONr_chiral_restr0.0960.23036
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0227620
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025840
X-RAY DIFFRACTIONr_nbd_refined0.2070.24718
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.220741
X-RAY DIFFRACTIONr_nbtor_refined0.1790.211850
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.210639
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.22208
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0690.24
X-RAY DIFFRACTIONr_metal_ion_refined0.0350.210
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1690.252
X-RAY DIFFRACTIONr_nbd_other0.2360.2281
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1850.2100
X-RAY DIFFRACTIONr_mcbond_it1.9112.211422
X-RAY DIFFRACTIONr_mcbond_other1.9112.19911421
X-RAY DIFFRACTIONr_mcangle_it2.4673.29314276
X-RAY DIFFRACTIONr_mcangle_other2.4673.29314277
X-RAY DIFFRACTIONr_scbond_it3.2782.48912569
X-RAY DIFFRACTIONr_scbond_other3.2782.48912570
X-RAY DIFFRACTIONr_scangle_it4.843.61218323
X-RAY DIFFRACTIONr_scangle_other4.843.61218324
X-RAY DIFFRACTIONr_lrange_it5.83227.18128168
X-RAY DIFFRACTIONr_lrange_other5.70426.50827409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.7650.26513580.24226303X-RAY DIFFRACTION99.9928
1.765-1.8130.24713200.2225650X-RAY DIFFRACTION99.9963
1.813-1.8660.22712530.19924969X-RAY DIFFRACTION99.9962
1.866-1.9230.21413020.19224134X-RAY DIFFRACTION99.9961
1.923-1.9860.20911800.1823487X-RAY DIFFRACTION100
1.986-2.0560.19711980.16922698X-RAY DIFFRACTION99.9916
2.056-2.1330.18111710.15421901X-RAY DIFFRACTION100
2.133-2.220.1810850.14821128X-RAY DIFFRACTION100
2.22-2.3190.17711030.14420178X-RAY DIFFRACTION99.9953
2.319-2.4320.1710090.13419386X-RAY DIFFRACTION100
2.432-2.5640.16310460.13218392X-RAY DIFFRACTION100
2.564-2.7190.1579340.12617420X-RAY DIFFRACTION99.9946
2.719-2.9070.168610.13116416X-RAY DIFFRACTION100
2.907-3.140.1578080.13615310X-RAY DIFFRACTION100
3.14-3.4390.1597580.14514118X-RAY DIFFRACTION100
3.439-3.8450.1576050.14112871X-RAY DIFFRACTION100
3.845-4.4390.1295170.12311392X-RAY DIFFRACTION100
4.439-5.4350.144640.1289668X-RAY DIFFRACTION99.9901
5.435-7.6790.164090.1527512X-RAY DIFFRACTION100
7.679-48.6210.1812060.1644281X-RAY DIFFRACTION99.4239

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