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- PDB-6phu: SpAga wild type apo structure -

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Basic information

Entry
Database: PDB / ID: 6phu
TitleSpAga wild type apo 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 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
L(+)-TARTARIC ACID / Alpha-galactosidase
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 4 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 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 1.4Oct 11, 2023Group: 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

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Assembly

Deposited unit
A: Alpha-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,2424
Polymers83,9681
Non-polymers2743
Water8,179454
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)336,97016
Polymers335,8734
Non-polymers1,09712
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 area26580 Å2
ΔGint-45 kcal/mol
Surface area85360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.724, 127.241, 151.820
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-988-

HOH

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Components

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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 4.6
Details: 0.1 M sodium acetate:acetic acid, 1.1 M ammonium tartrate 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 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 44566 / % possible obs: 99.2 % / Redundancy: 4.7 % / CC1/2: 0.986 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.077 / Net I/σ(I): 9
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3731 / CC1/2: 0.805 / Rpim(I) all: 0.244 / % possible all: 98.1

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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: 4FNU

4fnu


Resolution: 2.2→29.68 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.265 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.248 / ESU R Free: 0.203 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2334 2298 5.2 %RANDOM
Rwork0.1819 ---
obs0.1846 41959 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 93 Å2 / Biso mean: 34.826 Å2 / Biso min: 20.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.07 Å2
Refinement stepCycle: final / Resolution: 2.2→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5749 0 18 454 6221
Biso mean--41.77 36.21 -
Num. residues----722
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0125906
X-RAY DIFFRACTIONr_angle_refined_deg1.3381.6328008
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4315725
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.68823.545330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68215999
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4891530
X-RAY DIFFRACTIONr_chiral_restr0.1050.2751
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024575
LS refinement shellResolution: 2.2→2.255 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 174 -
Rwork0.222 2936 -
all-3110 -
obs--94.93 %

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