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- PDB-3a23: Crystal Structure of beta-L-Arabinopyranosidase complexed with D-... -

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Basic information

Entry
Database: PDB / ID: 3a23
TitleCrystal Structure of beta-L-Arabinopyranosidase complexed with D-galactose
ComponentsPutative secreted alpha-galactosidase
KeywordsHYDROLASE / beta-alpha-barrel / Greek key motif / beta-jellyroll / beta-trefoil
Function / homology
Function and homology information


alpha-galactosidase / alpha-galactosidase activity / carbohydrate metabolic process
Similarity search - Function
: / Alpha-galactosidase, CBM13 domain / Alpha galactosidase, C-terminal beta sandwich domain / Alpha galactosidase C-terminal beta sandwich domain / Alpha galactosidase A / Glycoside hydrolase, family 27 / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain ...: / Alpha-galactosidase, CBM13 domain / Alpha galactosidase, C-terminal beta sandwich domain / Alpha galactosidase C-terminal beta sandwich domain / Alpha galactosidase A / Glycoside hydrolase, family 27 / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Galactose-binding domain-like / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Aldolase class I / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-1PG / beta-D-galactopyranose / Alpha-galactosidase
Similarity search - Component
Biological speciesStreptomyces avermitilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFujimoto, Z. / Ichinose, H. / Kaneko, S.
Citation
Journal: J.Biol.Chem. / Year: 2009
Title: A beta-l-Arabinopyranosidase from Streptomyces avermitilis is a novel member of glycoside hydrolase family 27.
Authors: Ichinose, H. / Fujimoto, Z. / Honda, M. / Harazono, K. / Nishimoto, Y. / Uzura, A. / Kaneko, S.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Crystallization and preliminary crystallographic analysis of exo-alpha-1,5-L-arabinofuranosidase from Streptomyces avermitilis NBRC14893.
Authors: Fujimoto, Z. / Ichinose, H. / Kaneko, S.
History
DepositionApr 27, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 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: Putative secreted alpha-galactosidase
B: Putative secreted alpha-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,12932
Polymers128,6152
Non-polymers3,51330
Water26,7881487
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A: Putative secreted alpha-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,13318
Polymers64,3081
Non-polymers1,82617
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative secreted alpha-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,99514
Polymers64,3081
Non-polymers1,68813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.256, 99.081, 181.630
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 / Sugars , 2 types, 5 molecules AB

#1: Protein Putative secreted alpha-galactosidase


Mass: 64307.629 Da / Num. of mol.: 2 / Fragment: UNP residues 45-658
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avermitilis (bacteria) / Strain: NBRC14893 / Gene: agaA2, SAV2186, SAV_2186 / Plasmid: pIJ702 / Production host: Streptomyces lividans (bacteria) / Strain (production host): 1326 / References: UniProt: Q82L26
#2: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 1514 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H24O6
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1487 / 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: 2.39 Å3/Da / Density % sol: 48.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.7M ammonium sulfate, 1.7% PEG 400, 15% glycerol, 0.1M HEPES, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 97694 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 28.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 9.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.5.0088phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3A21

3a21


Resolution: 1.9→41.27 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.199 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17736 4876 5 %RANDOM
Rwork0.14225 ---
obs0.14402 92727 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2--0.01 Å20 Å2
3----0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.117 Å0.129 Å
Refinement stepCycle: LAST / Resolution: 1.9→41.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9032 0 222 1487 10741
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0219533
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1191.94113019
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.36151232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55824.934379
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.988151339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6171537
X-RAY DIFFRACTIONr_chiral_restr0.0760.21477
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217177
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.4671.56073
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.8429730
X-RAY DIFFRACTIONr_scbond_it1.34133460
X-RAY DIFFRACTIONr_scangle_it2.0834.53289
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.18 345 -
Rwork0.151 6646 -
obs--97.95 %

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