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- PDB-6gwg: Alpha-galactosidase from Thermotoga maritima in complex with cycl... -

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Basic information

Entry
Database: PDB / ID: 6gwg
TitleAlpha-galactosidase from Thermotoga maritima in complex with cyclohexene-based carbasugar mimic of galactose covalently linked to the nucleophile
ComponentsAlpha-galactosidase
KeywordsHYDROLASE / glycoside hydrolase / galactosidase / carbohydrate processing enzyme / inhibitor
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-FEK / Alpha-galactosidase
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsGloster, T.M. / Oehler, V.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Nat Commun / Year: 2018
Title: Revealing the mechanism for covalent inhibition of glycoside hydrolases by carbasugars at an atomic level.
Authors: Ren, W. / Pengelly, R. / Farren-Dai, M. / Shamsi Kazem Abadi, S. / Oehler, V. / Akintola, O. / Draper, J. / Meanwell, M. / Chakladar, S. / Swiderek, K. / Moliner, V. / Britton, R. / Gloster, T.M. / Bennet, A.J.
History
DepositionJun 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)67,40215
Polymers66,1981
Non-polymers1,20414
Water8,467470
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-117 kcal/mol
Surface area19970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.730, 95.870, 97.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alpha-galactosidase / Melibiase


Mass: 66198.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The electron density at the N- and C-terminus was disordered and the residues could not be modelled.
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: galA, TM_1192, Tmari_1199
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: G4FEF4, alpha-galactosidase

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Non-polymers , 5 types, 484 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FEK / (1~{S},2~{S},3~{S})-3-fluoranyl-6-(hydroxymethyl)cyclohex-5-ene-1,2,4-triol


Mass: 178.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11FO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.75 %
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: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.77→24.36 Å / Num. obs: 61617 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.074 / Net I/σ(I): 9
Reflection shellResolution: 1.77→1.82 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.438 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4481 / CC1/2: 0.564 / Rpim(I) all: 0.903 / % possible all: 56.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M0X

5m0x


Resolution: 1.77→24.36 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.262 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21495 2901 4.7 %RANDOM
Rwork0.16738 ---
obs0.16969 58648 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.819 Å2
Baniso -1Baniso -2Baniso -3
1-2.38 Å20 Å20 Å2
2---1.69 Å20 Å2
3----0.69 Å2
Refinement stepCycle: 1 / Resolution: 1.77→24.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4276 0 66 470 4812
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0144581
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174065
X-RAY DIFFRACTIONr_angle_refined_deg1.2071.6676243
X-RAY DIFFRACTIONr_angle_other_deg0.9151.6419556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4675571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.64722.143252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.94215777
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.991531
X-RAY DIFFRACTIONr_chiral_restr0.0710.2575
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025148
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02894
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_it2.6292.5772169
X-RAY DIFFRACTIONr_mcbond_other2.6262.5752168
X-RAY DIFFRACTIONr_mcangle_it3.3843.8512719
X-RAY DIFFRACTIONr_mcangle_other3.3833.8532720
X-RAY DIFFRACTIONr_scbond_it3.8342.9742412
X-RAY DIFFRACTIONr_scbond_other3.8342.9742412
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4754.3033504
X-RAY DIFFRACTIONr_long_range_B_refined6.81130.4185290
X-RAY DIFFRACTIONr_long_range_B_other6.8130.4145290
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 204 -
Rwork0.312 4260 -
obs--99.98 %

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