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- PDB-6nu8: Structure of sucrose-6-phosphate hydrolase from Lactobacillus gas... -

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Basic information

Entry
Database: PDB / ID: 6nu8
TitleStructure of sucrose-6-phosphate hydrolase from Lactobacillus gasseri in complex with fructose
ComponentsSucrose-6-phosphate hydrolase
KeywordsHYDROLASE / GH32 / glycoside hydrolase / Lactobacillus gasseri / fructose
Function / homology
Function and homology information


beta-fructofuranosidase activity / sucrose metabolic process / beta-fructofuranosidase / cytoplasm
Similarity search - Function
Sucrose-6-phosphate hydrolase / 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 / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
beta-D-fructofuranose / Sucrose-6-phosphate hydrolase
Similarity search - Component
Biological speciesLactobacillus gasseri 224-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLima, M.Z.T. / Muniz, J.R.C.
Funding support Brazil, 4items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2017/16291-5 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)309767/2015-6 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)486546/2013-6 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)308865/2018-9 Brazil
CitationJournal: To Be Published
Title: Structure of sucrose-6-phosphate hydrolase from Lactobacillus gasseri in complex with fructose
Authors: Lima, M.Z.T. / Muniz, J.R.C.
History
DepositionJan 31, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2020Group: Structure summary / Category: struct / Item: _struct.title
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 / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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: Sucrose-6-phosphate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8433
Polymers55,6011
Non-polymers2422
Water8,953497
1
A: Sucrose-6-phosphate hydrolase
hetero molecules

A: Sucrose-6-phosphate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,6866
Polymers111,2012
Non-polymers4844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area4110 Å2
ΔGint-5 kcal/mol
Surface area34870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.860, 103.860, 102.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-802-

HOH

21A-962-

HOH

31A-1071-

HOH

41A-1096-

HOH

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Components

#1: Protein Sucrose-6-phosphate hydrolase / Invertase


Mass: 55600.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus gasseri 224-1 (bacteria) / Gene: HMPREF9209_2365 / Production host: Escherichia coli (E. coli) / References: UniProt: D1YK18, beta-fructofuranosidase
#2: Sugar ChemComp-FRU / beta-D-fructofuranose / beta-D-fructose / D-fructose / fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DFrufbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fructofuranoseCOMMON NAMEGMML 1.0
b-D-FrufIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FruSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / 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: 2.47 Å3/Da / Density % sol: 50.27 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M buffer MMT pH 9.0; 25% (m/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4587 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4587 Å / Relative weight: 1
ReflectionResolution: 1.8→41.89 Å / Num. obs: 51784 / % possible obs: 99.1 % / Redundancy: 18 % / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.029 / Rrim(I) all: 0.096 / Net I/σ(I): 17
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2668 / CC1/2: 0.895 / Rpim(I) all: 0.209 / Rrim(I) all: 0.345 / % possible all: 88.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
TRUNCATEdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→41.89 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.669 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.092 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16532 2643 5.1 %RANDOM
Rwork0.13438 ---
obs0.13596 49110 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12.947 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.35 Å2
Refinement stepCycle: 1 / Resolution: 1.8→41.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3905 0 16 497 4418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0134092
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173517
X-RAY DIFFRACTIONr_angle_refined_deg1.8161.6425591
X-RAY DIFFRACTIONr_angle_other_deg1.5521.5818216
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7865507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.10424.103234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.29215636
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4611515
X-RAY DIFFRACTIONr_chiral_restr0.0980.2519
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024691
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02854
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_it0.9851.0261971
X-RAY DIFFRACTIONr_mcbond_other0.9851.0261970
X-RAY DIFFRACTIONr_mcangle_it1.5861.5332467
X-RAY DIFFRACTIONr_mcangle_other1.5861.5342468
X-RAY DIFFRACTIONr_scbond_it1.9291.2412121
X-RAY DIFFRACTIONr_scbond_other1.9281.2422122
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0431.7813115
X-RAY DIFFRACTIONr_long_range_B_refined4.89813.3494653
X-RAY DIFFRACTIONr_long_range_B_other4.68412.6214524
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 184 -
Rwork0.19 3198 -
obs--89.31 %
Refinement TLS params.Method: refined / Origin x: 16.081 Å / Origin y: -12.255 Å / Origin z: 21.634 Å
111213212223313233
T0.0162 Å20.0074 Å2-0.0049 Å2-0.0085 Å2-0.003 Å2--0.0025 Å2
L0.1424 °2-0.0234 °20.0187 °2-0.0997 °2-0.0482 °2--0.1089 °2
S-0.0054 Å °0.0035 Å °-0.0053 Å °0.0104 Å °0.0155 Å °-0.0002 Å °0.005 Å °0.0086 Å °-0.0101 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 28
2X-RAY DIFFRACTION1A29 - 141
3X-RAY DIFFRACTION1A142 - 175
4X-RAY DIFFRACTION1A176 - 198
5X-RAY DIFFRACTION1A199 - 272
6X-RAY DIFFRACTION1A273 - 340
7X-RAY DIFFRACTION1A341 - 366
8X-RAY DIFFRACTION1A367 - 460
9X-RAY DIFFRACTION1A461 - 489

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