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- PDB-6phv: SpAga galactose product complex structure -

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Basic information

Entry
Database: PDB / ID: 6phv
TitleSpAga galactose product complex structure
ComponentsAlpha-galactosidase
KeywordsHYDROLASE / (alpha/beta)8 barrel / glycoside hydrolase
Function / homology
Function and homology information


alpha-galactosidase / alpha-galactosidase activity / carbohydrate catabolic process
Similarity search - Function
alpha-galactosidase from lactobacil brevis / Glycosyl hydrolase family 36, N-terminal / Glycosyl hydrolase family 36, C-terminal / Alpha-galactosidase, N-terminal domain superfamily / Glycosyl hydrolase family 36 C-terminal domain / Glycosyl hydrolase family 36 N-terminal domain / Glycoside hydrolase family 36 / Melibiase / Glycoside hydrolase family 27/36, conserved site / Alpha-galactosidase signature. ...alpha-galactosidase from lactobacil brevis / Glycosyl hydrolase family 36, N-terminal / Glycosyl hydrolase family 36, C-terminal / Alpha-galactosidase, N-terminal domain superfamily / Glycosyl hydrolase family 36 C-terminal domain / Glycosyl hydrolase family 36 N-terminal domain / Glycoside hydrolase family 36 / Melibiase / Glycoside hydrolase family 27/36, conserved site / Alpha-galactosidase signature. / Beta-galactosidase; Chain A, domain 5 / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Distorted Sandwich / 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-D-galactopyranose / Alpha-galactosidase
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 4 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsPluvinage, B. / Boraston, A.B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Molecular analysis of an enigmaticStreptococcus pneumoniaevirulence factor: The raffinose-family oligosaccharide utilization system.
Authors: Hobbs, J.K. / Meier, E.P.W. / Pluvinage, B. / Mey, M.A. / Boraston, A.B.
History
DepositionJun 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 27, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 11, 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

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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)84,72811
Polymers83,9681
Non-polymers76010
Water9,152508
1
A: Alpha-galactosidase
hetero molecules

A: Alpha-galactosidase
hetero molecules

A: Alpha-galactosidase
hetero molecules

A: Alpha-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)338,91244
Polymers335,8734
Non-polymers3,03940
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area30380 Å2
ΔGint-22 kcal/mol
Surface area85100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.634, 127.283, 151.933
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1022-

HOH

21A-1270-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Alpha-galactosidase /


Mass: 83968.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) (bacteria)
Strain: ATCC BAA-334 / TIGR4 / Gene: aga, SP_1898 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2URQ6, alpha-galactosidase
#3: Sugar ChemComp-GLA / alpha-D-galactopyranose / alpha-D-galactose / D-galactose / galactose / ALPHA D-GALACTOSE / Galactose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 517 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 508 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.61 Å3/Da / Density % sol: 52.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.0 M sodium phosphate monobasic/potassium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.5419 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jan 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. obs: 50574 / % possible obs: 97.9 % / Redundancy: 3.5 % / CC1/2: 0.989 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.042 / Net I/σ(I): 14.8
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 3789 / CC1/2: 0.901 / Rpim(I) all: 0.189 / % possible all: 91.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PHU

6phu


Resolution: 2.1→24.77 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.278 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.207 / ESU R Free: 0.176 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2208 2486 5.1 %RANDOM
Rwork0.1761 ---
obs0.1784 46718 95.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 74.18 Å2 / Biso mean: 27.719 Å2 / Biso min: 15.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å20 Å2
2---0.14 Å20 Å2
3----0.24 Å2
Refinement stepCycle: final / Resolution: 2.1→24.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5752 0 49 509 6310
Biso mean--35.79 32.39 -
Num. residues----721
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0125924
X-RAY DIFFRACTIONr_angle_refined_deg1.2951.6358019
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2155722
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.33123.495329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.799151002
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8911530
X-RAY DIFFRACTIONr_chiral_restr0.0950.2752
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024553
LS refinement shellResolution: 2.098→2.152 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 187 -
Rwork0.201 3230 -
all-3417 -
obs--90.66 %

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