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

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Basic information

Entry
Database: PDB / ID: 6gvd
TitleAlpha-galactosidase from Thermotoga maritima in complex with cyclohexene-based carbasugar mimic of galactose
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 ...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-FDK / Alpha-galactosidase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsGloster, T.M. / Pengelly, R.J.
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 20, 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
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.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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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)66,6397
Polymers66,1981
Non-polymers4416
Water13,763764
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-51 kcal/mol
Surface area19980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.957, 96.135, 97.900
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 / Melibiase


Mass: 66198.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Electron density at the N- and C-terminus was disordered and could not be modelled in the structure.
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Gene: galA, TM_1192, Tmari_1199
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: G4FEF4, 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.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-FDK / (1~{S},2~{S},3~{S},4~{S})-5-(hydroxymethyl)cyclohex-5-ene-1,2,3,4-tetrol


Mass: 176.167 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H12O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 764 / 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: 2.38 Å3/Da / Density % sol: 48.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M MgSO4, 20% (w/v) poly(ethylene glycol) (PEG) 3350

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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 6M-F / 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: 1.22→68.59 Å / Num. obs: 185329 / % possible obs: 98.8 % / Redundancy: 5.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.029 / Net I/σ(I): 10.8
Reflection shellResolution: 1.22→1.25 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 12780 / CC1/2: 0.497 / Rpim(I) all: 0.506 / % possible all: 93.5

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Processing

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

5m0x


Resolution: 1.22→68.59 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.893 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18789 8840 4.8 %RANDOM
Rwork0.14913 ---
obs0.15097 173911 97.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.862 Å2
Baniso -1Baniso -2Baniso -3
1--2.36 Å20 Å20 Å2
2--0.81 Å20 Å2
3---1.55 Å2
Refinement stepCycle: 1 / Resolution: 1.22→68.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4281 0 25 764 5070
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0144691
X-RAY DIFFRACTIONr_bond_other_d00.0174232
X-RAY DIFFRACTIONr_angle_refined_deg1.2881.6566428
X-RAY DIFFRACTIONr_angle_other_deg0.991.6379976
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2655610
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.17922.706255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2915827
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0391528
X-RAY DIFFRACTIONr_chiral_restr0.0780.2593
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025341
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02914
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_it1.91.2012224
X-RAY DIFFRACTIONr_mcbond_other1.8471.1992223
X-RAY DIFFRACTIONr_mcangle_it2.3321.8112804
X-RAY DIFFRACTIONr_mcangle_other2.3321.8132805
X-RAY DIFFRACTIONr_scbond_it4.1671.5772467
X-RAY DIFFRACTIONr_scbond_other4.1661.5772468
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5482.213587
X-RAY DIFFRACTIONr_long_range_B_refined5.24316.1645409
X-RAY DIFFRACTIONr_long_range_B_other5.24316.1635410
X-RAY DIFFRACTIONr_rigid_bond_restr10.16638923
X-RAY DIFFRACTIONr_sphericity_free37.7165527
X-RAY DIFFRACTIONr_sphericity_bonded21.24759051
LS refinement shellResolution: 1.22→1.252 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 650 -
Rwork0.317 11723 -
obs--90.36 %

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