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

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Basic information

Entry
Database: PDB / ID: 5goo
TitleCrystal structure of alkaline invertase InvA from Anabaena sp. PCC 7120 complexed with fructose
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
beta-D-fructofuranose / beta-fructofuranosidase
Similarity search - Component
Biological speciesNostoc sp. PCC 7120 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.11 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 China 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 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _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: Alkaline Invertase
B: Alkaline Invertase
C: Alkaline Invertase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,7949
Polymers159,9783
Non-polymers8176
Water8,197455
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)321,58918
Polymers319,9556
Non-polymers1,63412
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area31870 Å2
ΔGint-164 kcal/mol
Surface area82100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.772, 177.927, 181.557
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-FRU / beta-D-fructofuranose / beta-D-fructose / D-fructose / fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 3
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / 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: 2.44 Å3/Da / Density % sol: 49.64 %
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: 2.1→50 Å / Num. obs: 87561 / % possible obs: 97.3 % / Redundancy: 6.3 % / Net I/σ(I): 25.9
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.9 % / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
PHENIXphasing
MOLREPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.11→31.79 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.803 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.174 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.218 4392 5 %RANDOM
Rwork0.193 ---
obs0.194 83084 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.24 Å2
Baniso -1Baniso -2Baniso -3
1-1.94 Å20 Å20 Å2
2---1.16 Å20 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 2.11→31.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10731 0 54 455 11240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01911076
X-RAY DIFFRACTIONr_bond_other_d0.0050.0210468
X-RAY DIFFRACTIONr_angle_refined_deg1.0441.97215023
X-RAY DIFFRACTIONr_angle_other_deg0.737324046
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.89851332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.1423.743529
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.756151723
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6211568
X-RAY DIFFRACTIONr_chiral_restr0.0570.21588
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02112503
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022659
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_it1.2073.4325337
X-RAY DIFFRACTIONr_mcbond_other1.2073.4315336
X-RAY DIFFRACTIONr_mcangle_it2.0355.146666
X-RAY DIFFRACTIONr_mcangle_other2.0355.1416667
X-RAY DIFFRACTIONr_scbond_it1.4673.6135734
X-RAY DIFFRACTIONr_scbond_other1.4673.6135734
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5065.3388354
X-RAY DIFFRACTIONr_long_range_B_refined3.9627.60513177
X-RAY DIFFRACTIONr_long_range_B_other3.9627.60613178
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.11→2.16 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 307 -
Rwork0.246 5582 -
obs--89.23 %

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