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- PDB-5m1i: Structure of GH36 alpha-galactosidase from Thermotoga maritima in... -

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Basic information

Entry
Database: PDB / ID: 5m1i
TitleStructure of GH36 alpha-galactosidase from Thermotoga maritima in a covalent complex with a cyclopropyl carbasugar.
ComponentsAlpha-galactosidase
KeywordsHYDROLASE / Alpha-galactosidase / glycoside hydrolase
Function / homology
Function and homology information


alpha-galactosidase / alpha-galactosidase activity / glycoside catabolic process / carbohydrate binding / carbohydrate metabolic process / protein homodimerization activity
Similarity search - Function
Immunoglobulin-like - #2760 / Alpha-galactosidase, N-terminal / Melibiase / : / Galactose mutarotase-like domain superfamily / Aldolase class I / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel ...Immunoglobulin-like - #2760 / Alpha-galactosidase, N-terminal / Melibiase / : / Galactose mutarotase-like domain superfamily / Aldolase class I / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-7D8 / Alpha-galactosidase / Alpha-galactosidase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsPengelly, R. / Gloster, T.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2016
Title: Structural Snapshots for Mechanism-Based Inactivation of a Glycoside Hydrolase by Cyclopropyl Carbasugars.
Authors: Adamson, C. / Pengelly, R.J. / Shamsi Kazem Abadi, S. / Chakladar, S. / Draper, J. / Britton, R. / Gloster, T.M. / Bennet, A.J.
History
DepositionOct 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Data collection / Structure summary
Revision 1.2Nov 30, 2016Group: Database references
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,69520
Polymers66,1981
Non-polymers1,49719
Water6,485360
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-44 kcal/mol
Surface area20650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.903, 96.239, 97.589
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Alpha-galactosidase


Mass: 66198.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: galA / Production host: Escherichia coli (E. coli)
References: UniProt: O33835, UniProt: G4FEF4*PLUS, alpha-galactosidase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-7D8 / (1~{R},2~{S},3~{S},4~{S},6~{R})-4-fluoranyl-1-(hydroxymethyl)bicyclo[4.1.0]heptane-2,3-diol


Mass: 176.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13FO3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.4 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium sulfate, 0.13 M ammonium citrate Protein was incubated with inhibitor at 333 K for 16 hours prior to crystallisation
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.55→68.52 Å / Num. obs: 92049 / % possible obs: 100 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 12.6
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.864 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
DIALSdata reduction
DIALSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M0X

5m0x


Resolution: 1.55→68.52 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.605 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18251 4568 5 %RANDOM
Rwork0.15357 ---
obs0.155 87347 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.906 Å2
Baniso -1Baniso -2Baniso -3
1-2.79 Å20 Å20 Å2
2---1.51 Å20 Å2
3----1.28 Å2
Refinement stepCycle: 1 / Resolution: 1.55→68.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4349 0 90 360 4799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0194687
X-RAY DIFFRACTIONr_bond_other_d0.0020.024390
X-RAY DIFFRACTIONr_angle_refined_deg1.681.9686360
X-RAY DIFFRACTIONr_angle_other_deg0.8263.00110139
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6615570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.68923.919222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.81915787
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9371530
X-RAY DIFFRACTIONr_chiral_restr0.1110.2673
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0215273
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021085
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8211.9742232
X-RAY DIFFRACTIONr_mcbond_other1.8211.9732231
X-RAY DIFFRACTIONr_mcangle_it2.4592.952815
X-RAY DIFFRACTIONr_mcangle_other2.4582.9512816
X-RAY DIFFRACTIONr_scbond_it3.9912.3892455
X-RAY DIFFRACTIONr_scbond_other3.9882.3892455
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8463.413542
X-RAY DIFFRACTIONr_long_range_B_refined6.42324.0245323
X-RAY DIFFRACTIONr_long_range_B_other6.42324.0325324
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 299 -
Rwork0.241 6418 -
obs--99.79 %

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