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- PDB-4eqv: Structure of Saccharomyces cerevisiae invertase -

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Basic information

Entry
Database: PDB / ID: 4eqv
TitleStructure of Saccharomyces cerevisiae invertase
ComponentsInvertase 2
KeywordsHYDROLASE / Glycosidase GH32 / Beta-Propeller / Carbohydrate/Sugar Binding
Function / homology
Function and homology information


fructan catabolic process / inulin catabolic process / inulinase activity / raffinose catabolic process / beta-fructofuranosidase activity / beta-fructofuranosidase / sucrose alpha-glucosidase activity / sucrose catabolic process / fungal-type vacuole / cell periphery ...fructan catabolic process / inulin catabolic process / inulinase activity / raffinose catabolic process / beta-fructofuranosidase activity / beta-fructofuranosidase / sucrose alpha-glucosidase activity / sucrose catabolic process / fungal-type vacuole / cell periphery / mitochondrion / extracellular region / cytoplasm
Similarity search - Function
Glycoside hydrolase, family 32, active site / Glycosyl hydrolases family 32 active site. / Glycosyl hydrolase family 32, C-terminal / Glycosyl hydrolases family 32 C terminal / Glycoside hydrolase, family 32 / Glycosyl hydrolase family 32, N-terminal / Glycosyl hydrolases family 32 N-terminal domain / Glycosyl hydrolases family 32 / Exo-inulinase; domain 1 / Glycosyl hydrolase domain; family 43 ...Glycoside hydrolase, family 32, active site / Glycosyl hydrolases family 32 active site. / Glycosyl hydrolase family 32, C-terminal / Glycosyl hydrolases family 32 C terminal / Glycoside hydrolase, family 32 / Glycosyl hydrolase family 32, N-terminal / Glycosyl hydrolases family 32 N-terminal domain / Glycosyl hydrolases family 32 / Exo-inulinase; domain 1 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsSainz-Polo, M.A. / Sanz-Aparicio, J.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Three-dimensional Structure of Saccharomyces Invertase: ROLE OF A NON-CATALYTIC DOMAIN IN OLIGOMERIZATION AND SUBSTRATE SPECIFICITY.
Authors: Sainz-Polo, M.A. / Ramirez-Escudero, M. / Lafraya, A. / Gonzalez, B. / Marin-Navarro, J. / Polaina, J. / Sanz-Aparicio, J.
History
DepositionApr 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2013Group: Database references
Revision 1.2Sep 13, 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

Downloads & links

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Assembly

Deposited unit
A: Invertase 2
B: Invertase 2
C: Invertase 2
D: Invertase 2
E: Invertase 2
F: Invertase 2
G: Invertase 2
H: Invertase 2


Theoretical massNumber of molelcules
Total (without water)468,6908
Polymers468,6908
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)268.659, 268.659, 224.452
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.711051, 0.700977, -0.055115), (0.700998, -0.712818, -0.022195), (-0.054845, -0.022854, -0.998233)-97.95715, 229.09407, -129.70535
3given(-0.713918, -0.700218, 0.003913), (-0.700216, 0.713928, 0.002198), (-0.004333, -0.00117, -0.99999)-175.67973, -71.46441, -124.04752
4given(-0.998245, 0.000962, 0.059214), (0.000324, -0.999764, 0.021713), (0.059221, 0.021694, 0.998009)-266.13, 159.77669, 5.4562

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Components

#1: Protein
Invertase 2 / Beta-fructofuranosidase 2 / Saccharase


Mass: 58586.242 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SUC2, YIL162W / Plasmid: pRARE2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00724, beta-fructofuranosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 4.99 Å3/Da / Density % sol: 75.35 %
Crystal growTemperature: 293 K / pH: 6.5
Details: 3% PEG 3350, 5% MPD, 0.6M Magnesium formate, 1mM TCEP, 75 mM Guanidinium chloride, 0.1 Bis-Tris pH 6.5 (2:1), VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0666
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0666 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.73
11-h,-k,l20.27
ReflectionResolution: 3.3→56.31 Å / Num. obs: 137870 / % possible obs: 98.5 % / Observed criterion σ(I): 1 / Redundancy: 6.4 % / Biso Wilson estimate: 66.21 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 8.1
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 5 % / Rmerge(I) obs: 0.798 / Mean I/σ(I) obs: 2 / Rsym value: 0.377 / % possible all: 92.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KF3

3kf3


Resolution: 3.4→56.31 Å / Cor.coef. Fo:Fc: 0.814 / Cor.coef. Fo:Fc free: 0.787 / SU B: 23.718 / SU ML: 0.374 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.239 6361 5 %RANDOM
Rwork0.221 ---
obs0.222 137870 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2---0.25 Å20 Å2
3---0.49 Å2
Refinement stepCycle: LAST / Resolution: 3.4→56.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32992 0 0 24 33016
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0234016
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1761.92246384
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.52254064
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.27424.9331784
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.031155144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.47815104
X-RAY DIFFRACTIONr_chiral_restr0.0830.24784
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02127016
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.4→3.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 433 -
Rwork0.245 8135 -
obs--91.11 %

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