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- PDB-5m16: Structure of GH36 alpha-galactosidase from Thermotoga maritima in... -

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Basic information

Entry
Database: PDB / ID: 5m16
TitleStructure of GH36 alpha-galactosidase from Thermotoga maritima in complex with a hydrolysed 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 ...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-7D2 / Alpha-galactosidase / Alpha-galactosidase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 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 30, 2016Group: Database references
Revision 1.2Jan 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)66,6055
Polymers66,1981
Non-polymers4074
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint-37 kcal/mol
Surface area20230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.300, 96.020, 98.050
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.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-7D2 / (1~{R},2~{S},3~{S},4~{S},5~{S},6~{S})-1-(hydroxymethyl)bicyclo[4.1.0]heptane-2,3,4,5-tetrol


Mass: 190.194 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H14O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.43 Å3/Da / Density % sol: 49.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M magnesium sulfate, 20% (w/v) PEG 3350 Crystals were soaked for 7 days in 1 mM inhibitor, 30% (w/v) PEG 3350 before freezing.
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.62→55.66 Å / Num. obs: 82206 / % possible obs: 99.6 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 15.8
Reflection shellResolution: 1.62→1.66 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 2.4 / % possible all: 99.7

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Processing

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

5m0x


Resolution: 1.62→55.66 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.069 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19788 4059 4.9 %RANDOM
Rwork0.1722 ---
obs0.17351 78077 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.183 Å2
Baniso -1Baniso -2Baniso -3
1-3.26 Å20 Å20 Å2
2---1.45 Å20 Å2
3----1.81 Å2
Refinement stepCycle: 1 / Resolution: 1.62→55.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4316 0 24 355 4695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0194570
X-RAY DIFFRACTIONr_bond_other_d0.0010.024247
X-RAY DIFFRACTIONr_angle_refined_deg1.6071.9586222
X-RAY DIFFRACTIONr_angle_other_deg0.8473.0019809
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9755556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.61124225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.16315769
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.641530
X-RAY DIFFRACTIONr_chiral_restr0.110.2658
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0215193
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021073
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_it2.3332.1552191
X-RAY DIFFRACTIONr_mcbond_other2.3312.1542190
X-RAY DIFFRACTIONr_mcangle_it3.0163.222758
X-RAY DIFFRACTIONr_mcangle_other3.0163.2222759
X-RAY DIFFRACTIONr_scbond_it3.6682.5022379
X-RAY DIFFRACTIONr_scbond_other3.6682.5022380
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1953.6073462
X-RAY DIFFRACTIONr_long_range_B_refined5.98925.2225072
X-RAY DIFFRACTIONr_long_range_B_other5.98825.2225073
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.62→1.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 276 -
Rwork0.273 5763 -
obs--99.65 %

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