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- PDB-5gop: Crystal structure of alkaline invertase InvA from Anabaena sp. PC... -

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Basic information

Entry
Database: PDB / ID: 5gop
TitleCrystal structure of alkaline invertase InvA from Anabaena sp. PCC 7120 complexed with sucrose
ComponentsAlkaline Invertase
KeywordsHYDROLASE / alkaline invertases / cyanobacteria / glycoside hydrolase family 100 / sucrose hydrolysis
Function / homology
Function and homology information


endo-alpha-N-acetylgalactosaminidase activity / beta-fructofuranosidase / sucrose alpha-glucosidase activity / sucrose catabolic process
Similarity search - Function
Glycosyl hydrolase family 100 / Alkaline and neutral invertase / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
sucrose / beta-D-fructofuranose / beta-fructofuranosidase
Similarity search - Component
Biological speciesNostoc sp. PCC 7120 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsXie, J. / Cai, K. / Hu, H.X. / Jiang, Y.L. / Yang, F. / Hu, P.F. / Chen, Y. / Zhou, C.Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31370757 China
CitationJournal: J. Biol. Chem. / Year: 2016
Title: Structural Analysis of the Catalytic Mechanism and Substrate Specificity of Anabaena Alkaline Invertase InvA Reveals a Novel Glucosidase
Authors: Xie, J. / Cai, K. / Hu, H.X. / Jiang, Y.L. / Yang, F. / Hu, P.F. / Cao, D.D. / Li, W.F. / Chen, Y. / Zhou, C.Z.
History
DepositionJul 28, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 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
Revision 2.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alkaline Invertase
B: Alkaline Invertase
C: Alkaline Invertase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,8426
Polymers159,9783
Non-polymers8653
Water6,035335
1
A: Alkaline Invertase
B: Alkaline Invertase
C: Alkaline Invertase
hetero molecules

A: Alkaline Invertase
B: Alkaline Invertase
C: Alkaline Invertase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)321,68512
Polymers319,9556
Non-polymers1,7296
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area29190 Å2
ΔGint-157 kcal/mol
Surface area81600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.866, 178.923, 181.324
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Alkaline Invertase / Alr1521 protein


Mass: 53325.844 Da / Num. of mol.: 3 / Fragment: UNP residues 9-460
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. PCC 7120 (bacteria) / Strain: PCC 7120 / Gene: invA, alr1521 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YWS9, beta-fructofuranosidase
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.53 Å3/Da / Density % sol: 51.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 1.5 M Lithium sulfate, 0.1 M Tris / PH range: 8-8.5 / Temp details: 287 K first, then transfer to 298 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 27, 2016
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 67492 / % possible obs: 98.5 % / Redundancy: 3.8 % / Net I/σ(I): 17.2
Reflection shellResolution: 2.34→2.43 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.9 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
MOLREPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GOO

5goo


Resolution: 2.35→33.941 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2353 3381 5.06 %RANDOM
Rwork0.2066 ---
obs0.208 66778 98.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→33.941 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10610 0 58 335 11003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410978
X-RAY DIFFRACTIONf_angle_d1.08414904
X-RAY DIFFRACTIONf_dihedral_angle_d13.2593975
X-RAY DIFFRACTIONf_chiral_restr0.1211578
X-RAY DIFFRACTIONf_plane_restr0.0041907
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.38360.29281450.27482659X-RAY DIFFRACTION99
2.3836-2.41910.32091440.2562634X-RAY DIFFRACTION100
2.4191-2.45690.30271600.25622590X-RAY DIFFRACTION99
2.4569-2.49720.25561410.25562661X-RAY DIFFRACTION99
2.4972-2.54020.27971370.24732632X-RAY DIFFRACTION100
2.5402-2.58640.26541360.24012628X-RAY DIFFRACTION99
2.5864-2.63620.28271550.25142678X-RAY DIFFRACTION99
2.6362-2.68990.27971540.24632599X-RAY DIFFRACTION100
2.6899-2.74840.30461170.23942656X-RAY DIFFRACTION99
2.7484-2.81230.25571440.23562647X-RAY DIFFRACTION99
2.8123-2.88260.27871500.23272624X-RAY DIFFRACTION99
2.8826-2.96050.27721480.23182634X-RAY DIFFRACTION99
2.9605-3.04760.24761300.21612645X-RAY DIFFRACTION99
3.0476-3.14590.26051310.23072664X-RAY DIFFRACTION99
3.1459-3.25820.23911520.22512610X-RAY DIFFRACTION99
3.2582-3.38860.29081620.22142632X-RAY DIFFRACTION99
3.3886-3.54260.20511300.20642651X-RAY DIFFRACTION98
3.5426-3.72920.21741440.19052622X-RAY DIFFRACTION98
3.7292-3.96250.1781140.18432681X-RAY DIFFRACTION98
3.9625-4.26790.21351440.17622643X-RAY DIFFRACTION98
4.2679-4.69640.18671300.1682606X-RAY DIFFRACTION97
4.6964-5.37360.21071260.1762660X-RAY DIFFRACTION97
5.3736-6.76140.23571490.20742642X-RAY DIFFRACTION97
6.7614-33.94490.18841380.17722699X-RAY DIFFRACTION94

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