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- PDB-5m0x: Structure of apo structure of GH36 alpha-galactosidase from Therm... -

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Basic information

Entry
Database: PDB / ID: 5m0x
TitleStructure of apo structure of GH36 alpha-galactosidase from Thermotoga maritima
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
Alpha-galactosidase / Alpha-galactosidase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 6, 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)66,5115
Polymers66,1981
Non-polymers3124
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint-47 kcal/mol
Surface area20150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.960, 95.780, 97.540
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
Details: Differences at the N-terminus arise from the vector used for expression (primarily a His tag). Differences at the C-terminus arise from the lack of electron density meaning this part could not be modelled.
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 48.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M magnesium sulfate, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 1.8→32.09 Å / Num. obs: 59066 / % possible obs: 99 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.9
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.706 / Mean I/σ(I) obs: 2.6 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
Aimlessdata scaling
xia2data reduction
XDSdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZY9

1zy9


Resolution: 1.8→32.09 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.278 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.126 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23128 2938 5.1 %RANDOM
Rwork0.18613 ---
obs0.18845 55012 97.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.643 Å2
Baniso -1Baniso -2Baniso -3
1-4.74 Å20 Å20 Å2
2---2.2 Å20 Å2
3----2.54 Å2
Refinement stepCycle: 1 / Resolution: 1.8→32.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4311 0 16 328 4655
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0194534
X-RAY DIFFRACTIONr_bond_other_d0.0020.024239
X-RAY DIFFRACTIONr_angle_refined_deg1.7951.9576163
X-RAY DIFFRACTIONr_angle_other_deg1.01439783
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.615550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.87623.846221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38215770
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3951530
X-RAY DIFFRACTIONr_chiral_restr0.1110.2649
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215127
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021065
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_it2.3142.7052173
X-RAY DIFFRACTIONr_mcbond_other2.3072.7032172
X-RAY DIFFRACTIONr_mcangle_it3.1634.0462729
X-RAY DIFFRACTIONr_mcangle_other3.1624.0482730
X-RAY DIFFRACTIONr_scbond_it3.2993.0852361
X-RAY DIFFRACTIONr_scbond_other3.2563.072347
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9764.4543415
X-RAY DIFFRACTIONr_long_range_B_refined6.2731.8545194
X-RAY DIFFRACTIONr_long_range_B_other6.23431.6175140
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 209 -
Rwork0.271 3644 -
obs--88.76 %

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