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- PDB-6nu7: Structure of sucrose-6-phosphate hydrolase from Lactobacillus gasseri -

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Basic information

Entry
Database: PDB / ID: 6nu7
TitleStructure of sucrose-6-phosphate hydrolase from Lactobacillus gasseri
ComponentsSucrose-6-phosphate hydrolase
KeywordsHYDROLASE / GH32 / glycoside hydrolase / Lactobacillus gasseri
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
Sucrose-6-phosphate hydrolase
Similarity search - Component
Biological speciesLactobacillus gasseri 224-1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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
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 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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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)55,9557
Polymers55,6011
Non-polymers3546
Water12,484693
1
A: Sucrose-6-phosphate hydrolase
hetero molecules

A: Sucrose-6-phosphate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,91014
Polymers111,2012
Non-polymers70912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area5260 Å2
ΔGint-27 kcal/mol
Surface area34370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.149, 103.149, 101.978
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-601-

HOH

21A-760-

HOH

31A-855-

HOH

41A-999-

HOH

51A-1121-

HOH

61A-1273-

HOH

71A-1284-

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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 693 / 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: 2.44 Å3/Da / Density % sol: 49.58 %
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: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Jul 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→72.94 Å / Num. obs: 44022 / % possible obs: 99.9 % / Redundancy: 31.6 % / CC1/2: 0.988 / Rmerge(I) obs: 0.287 / Rpim(I) all: 0.075 / Rrim(I) all: 0.297 / Χ2: 1.02 / Net I/σ(I): 13.7
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 15 % / Rmerge(I) obs: 0.961 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 2755 / CC1/2: 0.719 / Rpim(I) all: 0.367 / Rrim(I) all: 1.024 / Χ2: 1.17 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
Aimlessdata scaling
SAINTdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PIG

3pig


Resolution: 1.9→46.023 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.68
RfactorNum. reflection% reflection
Rfree0.2034 2370 5.4 %
Rwork0.1656 --
obs0.1676 43900 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→46.023 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3891 0 22 693 4606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114067
X-RAY DIFFRACTIONf_angle_d1.0165550
X-RAY DIFFRACTIONf_dihedral_angle_d3.2083282
X-RAY DIFFRACTIONf_chiral_restr0.065577
X-RAY DIFFRACTIONf_plane_restr0.006737
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.93770.27471470.23372369X-RAY DIFFRACTION98
1.9377-1.97980.26661580.20722355X-RAY DIFFRACTION100
1.9798-2.02590.19621360.19872432X-RAY DIFFRACTION100
2.0259-2.07660.23211270.18812410X-RAY DIFFRACTION100
2.0766-2.13270.25021630.17112403X-RAY DIFFRACTION100
2.1327-2.19550.20341610.16532390X-RAY DIFFRACTION100
2.1955-2.26630.20611630.1642393X-RAY DIFFRACTION100
2.2663-2.34730.20711120.15752448X-RAY DIFFRACTION100
2.3473-2.44130.22051500.16532409X-RAY DIFFRACTION100
2.4413-2.55240.21661090.16642466X-RAY DIFFRACTION100
2.5524-2.68690.21321090.16172469X-RAY DIFFRACTION100
2.6869-2.85530.19631360.16642453X-RAY DIFFRACTION100
2.8553-3.07570.22921260.16682465X-RAY DIFFRACTION100
3.0757-3.38510.20031290.14682468X-RAY DIFFRACTION100
3.3851-3.87470.15611650.14082446X-RAY DIFFRACTION99
3.8747-4.88090.13681260.1232510X-RAY DIFFRACTION99
4.8809-46.0370.18241530.17122644X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 12.2691 Å / Origin y: 15.8449 Å / Origin z: 21.7628 Å
111213212223313233
T0.0208 Å2-0.0042 Å20.0129 Å2-0.0143 Å2-0.0145 Å2--0.0197 Å2
L0.4875 °20.0198 °20.0463 °2-0.424 °20.0103 °2--0.5565 °2
S0.0165 Å °-0.0034 Å °0.0202 Å °-0.0037 Å °0.0012 Å °-0.0163 Å °-0.0429 Å °0.0294 Å °-0.0053 Å °
Refinement TLS groupSelection details: all

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