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- PDB-9h8i: Crystallization of B. licheniformis levanase -

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Basic information

Entry
Database: PDB / ID: 9h8i
TitleCrystallization of B. licheniformis levanase
ComponentsEndolevansase LevB1
KeywordsSTRUCTURAL PROTEIN / Levanase B. licheniformis
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
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsCarr, S. / Cruz-Migoni, A. / Porras-Dominguez, J.R. / Van den Ende, W. / Lopez-Munguia Canales, A.
Funding support Mexico, 1items
OrganizationGrant numberCountry
Other governmentDGAPA-UNAM IT200316 Mexico
CitationJournal: J.Agric.Food Chem. / Year: 2025
Title: Understanding the Endo- and Exo-mechanisms Involved in the Enzymatic Hydrolysis of Levan and Inulin Polymers.
Authors: Porras-Dominguez, J.R. / Cruz-Migoni, A. / Carr, S.B. / Rodriguez-Alegria, M.E. / Lopez-Munguia, A. / Van den Ende, W.
History
DepositionOct 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endolevansase LevB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0077
Polymers55,4761
Non-polymers5316
Water4,360242
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: none
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-19 kcal/mol
Surface area19610 Å2
Unit cell
Length a, b, c (Å)82.586, 82.586, 171.088
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-741-

HOH

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Components

#1: Protein Endolevansase LevB1


Mass: 55476.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Gene: levB / Production host: Escherichia coli (E. coli) / References: UniProt: W8GV60
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.87 Å3/Da / Density % sol: 57.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 10% w/v PEG 8000, 20% v/v ethylene glycol and 0.03 M Magnesium chloride, calcium chloride and 0.1 M bicine/Trizma base pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.5→74.375 Å / Num. obs: 85690 / % possible obs: 97.1 % / Redundancy: 26.1 % / CC1/2: 0.999 / Net I/σ(I): 15.9
Reflection shellResolution: 1.54→1.57 Å / Num. unique obs: 4130 / CC1/2: 0.639 / Rpim(I) all: 0.698

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata reduction
MrBUMPphasing
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4fff

4fff


Resolution: 1.54→74.375 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.192 / WRfactor Rwork: 0.172 / SU B: 1.619 / SU ML: 0.055 / Average fsc free: 0.9578 / Average fsc work: 0.9662 / Cross valid method: FREE R-VALUE / ESU R: 0.074 / ESU R Free: 0.075
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2169 4272 5.007 %
Rwork0.1928 81042 -
all0.194 --
obs-85314 96.772 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 23.445 Å2
Baniso -1Baniso -2Baniso -3
1--0.132 Å20 Å20 Å2
2---0.132 Å20 Å2
3---0.263 Å2
Refinement stepCycle: LAST / Resolution: 1.54→74.375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3583 0 32 242 3857
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123713
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163289
X-RAY DIFFRACTIONr_angle_refined_deg1.8151.8125033
X-RAY DIFFRACTIONr_angle_other_deg0.631.7787588
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1975443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.503517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.52910578
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.39810198
X-RAY DIFFRACTIONr_chiral_restr0.0940.2511
X-RAY DIFFRACTIONr_chiral_restr_other00.21
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024476
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02910
X-RAY DIFFRACTIONr_nbd_refined0.1980.2607
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.23002
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21753
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.21914
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2195
X-RAY DIFFRACTIONr_metal_ion_refined0.0910.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.380.212
X-RAY DIFFRACTIONr_nbd_other0.2680.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0990.29
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0040.22
X-RAY DIFFRACTIONr_mcbond_it2.5332.2011778
X-RAY DIFFRACTIONr_mcbond_other2.5092.21778
X-RAY DIFFRACTIONr_mcangle_it3.7053.932216
X-RAY DIFFRACTIONr_mcangle_other3.7093.9332217
X-RAY DIFFRACTIONr_scbond_it4.1932.6821935
X-RAY DIFFRACTIONr_scbond_other4.1922.6821936
X-RAY DIFFRACTIONr_scangle_it6.4814.7072816
X-RAY DIFFRACTIONr_scangle_other6.484.7072817
X-RAY DIFFRACTIONr_lrange_it8.62723.1274045
X-RAY DIFFRACTIONr_lrange_other8.62623.1274046
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.54-1.580.3393060.34357480.34264120.9180.9294.41670.332
1.58-1.6230.3412810.33956570.33962800.9250.92894.55410.322
1.623-1.670.373160.30954480.31360650.9130.93995.03710.283
1.67-1.7220.2892990.2853780.28159510.9480.95295.39570.248
1.722-1.7780.2752490.24252330.24357180.9550.96395.87270.207
1.778-1.840.2542740.2250970.22255830.960.96996.20280.183
1.84-1.910.2442490.20649220.20753640.9620.97496.40190.171
1.91-1.9880.2262440.19147770.19351850.970.97796.8370.161
1.988-2.0760.2192470.18346030.18549930.9720.9897.1360.159
2.076-2.1770.2162380.17744120.17947800.9730.98197.28030.156
2.177-2.2950.1862100.17442310.17545520.980.98297.56150.154
2.295-2.4340.1972370.16339870.16543150.9760.98497.89110.144
2.434-2.6020.1862120.16337820.16440690.9780.98498.15680.144
2.602-2.810.1871720.1635490.16237840.9790.98498.33510.143
2.81-3.0780.1971820.17332860.17435180.9730.98198.57870.159
3.078-3.4410.1861590.17830140.17832130.9770.98198.75510.172
3.441-3.9710.2151380.17626690.17828360.9740.98298.97740.175
3.971-4.8610.1651160.15223180.15324510.9840.98899.30640.157
4.861-6.8590.174920.20318300.20219320.9830.98599.48240.204
6.859-74.3750.332510.23911030.24311610.9050.95799.39710.239

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