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- PDB-8i12: InuAMN8 -

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Basic information

Entry
Database: PDB / ID: 8i12
TitleInuAMN8
ComponentsGlycosyl hydrolase family 32 exo-inulinase
KeywordsHYDROLASE / Cold-active / NaCl-tolerant / exo-inulinase
Function / homology
Function and homology information


sucrose alpha-glucosidase activity / sucrose catabolic process / cytoplasm
Similarity search - Function
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
DI(HYDROXYETHYL)ETHER / Glycosyl hydrolase family 32 exo-inulinase
Similarity search - Component
Biological speciesArthrobacter sp. MN8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsZhou, J.P. / Cen, X.L. / He, L.M. / Zhang, R. / Huang, Z.X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cold-active and NaCl-tolerant exo-inulinase InuAMN8.
Authors: Cen, X.L. / He, L.M. / Zhang, R. / Huang, Z.X. / Zhou, J.P.
History
DepositionJan 12, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyl hydrolase family 32 exo-inulinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7336
Polymers57,2451
Non-polymers4895
Water11,998666
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.630, 79.220, 94.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Glycosyl hydrolase family 32 exo-inulinase


Mass: 57244.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter sp. MN8 (bacteria) / Gene: inuA / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A0F6MV26
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#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 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 666 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.02 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: JCSG4-60 0.1 M HEPES pH 6.5, 30% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 20, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.36→94.57 Å / Num. obs: 99430 / % possible obs: 99.3 % / Redundancy: 12.2 % / Biso Wilson estimate: 7.89 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 26.7
Reflection shellResolution: 1.36→1.39 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.111 / Mean I/σ(I) obs: 7.4 / Num. unique obs: 9000 / % possible all: 91.3

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Processing

Software
NameVersionClassification
PHENIX1.10.1-2155refinement
DIALS3.7.2data reduction
DIALS3.7.2data scaling
PHENIX10.1-2155phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36→48.64 Å / SU ML: 0.1035 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 12.5827
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1494 2000 2.01 %
Rwork0.1243 97289 -
obs0.1248 99289 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.73 Å2
Refinement stepCycle: LAST / Resolution: 1.36→48.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3791 0 32 666 4489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01284059
X-RAY DIFFRACTIONf_angle_d1.38565546
X-RAY DIFFRACTIONf_chiral_restr0.2016574
X-RAY DIFFRACTIONf_plane_restr0.0098742
X-RAY DIFFRACTIONf_dihedral_angle_d21.9231449
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.390.15291300.1036305X-RAY DIFFRACTION90.98
1.39-1.430.16241410.10296890X-RAY DIFFRACTION99.36
1.43-1.470.14051410.10096893X-RAY DIFFRACTION99.97
1.47-1.520.14561440.09696942X-RAY DIFFRACTION99.99
1.52-1.570.14271420.0936947X-RAY DIFFRACTION99.99
1.57-1.640.12561420.09836940X-RAY DIFFRACTION100
1.64-1.710.15591440.10676976X-RAY DIFFRACTION99.99
1.71-1.80.14291440.11236964X-RAY DIFFRACTION99.99
1.8-1.920.14091430.11666983X-RAY DIFFRACTION100
1.92-2.060.15221440.11976991X-RAY DIFFRACTION99.97
2.06-2.270.13121440.12067012X-RAY DIFFRACTION99.99
2.27-2.60.15011440.13997058X-RAY DIFFRACTION99.99
2.6-3.280.16611470.14467123X-RAY DIFFRACTION99.96
3.28-3.560.15541500.14587265X-RAY DIFFRACTION98.54

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