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- PDB-5z73: Crystal structure of alkaline/neutral invertase InvB from Anabaen... -

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Basic information

Entry
Database: PDB / ID: 5z73
TitleCrystal structure of alkaline/neutral invertase InvB from Anabaena sp. PCC 7120
ComponentsAlr0819 protein
KeywordsHYDROLASE / alkaline/neutral invertases / cyanobacteria / glycoside hydrolase family 100 / sucrose hydrolysis
Function / homologyGlycosyl hydrolase family 100 / Alkaline and neutral invertase / endo-alpha-N-acetylgalactosaminidase activity / beta-fructofuranosidase / sucrose alpha-glucosidase activity / sucrose catabolic process / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / beta-fructofuranosidase
Function and homology information
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.93 Å
AuthorsXie, J. / Hu, H.X. / Cai, K. / Yang, F. / Jiang, Y.L. / Chen, Y. / Zhou, C.Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31630001 China
CitationJournal: FEBS Lett. / Year: 2018
Title: Structural and enzymatic analyses of Anabaena heterocyst-specific alkaline invertase InvB.
Authors: Xie, J. / Hu, H.X. / Cai, K. / Xia, L.Y. / Yang, F. / Jiang, Y.L. / Chen, Y. / Zhou, C.Z.
History
DepositionJan 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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: Alr0819 protein
B: Alr0819 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,3113
Polymers105,2192
Non-polymers921
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-32 kcal/mol
Surface area30870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.637, 82.384, 94.829
Angle α, β, γ (deg.)90.00, 118.86, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Alr0819 protein / Neutral invertase


Mass: 52609.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / Gene: invB, alr0819 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YYM9, beta-fructofuranosidase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.71 Å3/Da / Density % sol: 54.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.7M lithium chloride, 6% polyethylene glycol 6000, 0.1M MES, pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / 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: 1.93→50 Å / Num. obs: 82269 / % possible obs: 97.6 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 15.1
Reflection shellResolution: 1.93→2 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 8274 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data collection
RefinementMethod to determine structure: SAD / Resolution: 1.93→31.41 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.659 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.137 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22767 4096 5 %RANDOM
Rwork0.20431 ---
obs0.2055 78169 97.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.334 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å2-0 Å20.31 Å2
2--1.03 Å20 Å2
3----0.1 Å2
Refinement stepCycle: 1 / Resolution: 1.93→31.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6913 0 6 287 7206
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0197085
X-RAY DIFFRACTIONr_bond_other_d0.0050.026802
X-RAY DIFFRACTIONr_angle_refined_deg0.9141.9789611
X-RAY DIFFRACTIONr_angle_other_deg0.706315624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6125853
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.123.804326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.217151145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6181546
X-RAY DIFFRACTIONr_chiral_restr0.0540.21049
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217915
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021631
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_it1.1284.0553433
X-RAY DIFFRACTIONr_mcbond_other1.1284.0553432
X-RAY DIFFRACTIONr_mcangle_it1.9636.0664279
X-RAY DIFFRACTIONr_mcangle_other1.9636.0674280
X-RAY DIFFRACTIONr_scbond_it1.0564.2453652
X-RAY DIFFRACTIONr_scbond_other1.0564.2453652
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8426.2975333
X-RAY DIFFRACTIONr_long_range_B_refined3.31832.9668475
X-RAY DIFFRACTIONr_long_range_B_other3.25232.898373
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.931→1.981 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 304 -
Rwork0.281 5738 -
obs--97.85 %

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