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

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Basic information

Entry
Database: PDB / ID: 5goq
TitleCrystal structure of alkaline invertase InvA from Anabaena sp. PCC 7120 complexed with glucose
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
alpha-D-glucopyranose / beta-fructofuranosidase
Similarity search - Component
Biological speciesNostoc sp. PCC 7120 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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 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 / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 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 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)160,5186
Polymers159,9783
Non-polymers5403
Water1,874104
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)321,03612
Polymers319,9556
Non-polymers1,0816
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area28000 Å2
ΔGint-162 kcal/mol
Surface area83290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.515, 179.094, 181.562
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: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.45 Å3/Da / Density % sol: 49.84 %
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: BL18U1 / Wavelength: 0.97791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 24, 2016
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97791 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 38985 / % possible obs: 94.5 % / Redundancy: 8.8 % / Net I/σ(I): 18
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 2.8 / % possible all: 96.1

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Processing

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

5goo


Resolution: 2.75→48.895 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1948 5.01 %RANDOM
Rwork0.1868 ---
obs0.1891 38906 94.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→48.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10547 0 36 104 10687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710894
X-RAY DIFFRACTIONf_angle_d1.09614777
X-RAY DIFFRACTIONf_dihedral_angle_d13.2463958
X-RAY DIFFRACTIONf_chiral_restr0.0511564
X-RAY DIFFRACTIONf_plane_restr0.0071895
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7501-2.81880.3141480.26922621X-RAY DIFFRACTION96
2.8188-2.8950.26841380.23732679X-RAY DIFFRACTION96
2.895-2.98020.31421450.2282626X-RAY DIFFRACTION96
2.9802-3.07640.31051220.22232671X-RAY DIFFRACTION96
3.0764-3.18630.28281500.22812639X-RAY DIFFRACTION95
3.1863-3.31390.2811190.21952663X-RAY DIFFRACTION95
3.3139-3.46470.26531350.20212636X-RAY DIFFRACTION95
3.4647-3.64730.20311560.17842633X-RAY DIFFRACTION95
3.6473-3.87570.20391440.16722616X-RAY DIFFRACTION94
3.8757-4.17480.18981390.16522633X-RAY DIFFRACTION94
4.1748-4.59460.20261370.15232651X-RAY DIFFRACTION94
4.5946-5.25880.20681580.16122602X-RAY DIFFRACTION93
5.2588-6.62290.23481240.18832616X-RAY DIFFRACTION92
6.6229-48.90280.22681330.17782672X-RAY DIFFRACTION90

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