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- PDB-6lnr: Structure of intact chitinase with hevein domain from the plant S... -

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Basic information

Entry
Database: PDB / ID: 6lnr
TitleStructure of intact chitinase with hevein domain from the plant Simarouba glauca, known for its traditional anti-inflammatory efficacy
ComponentsClass-1 chitinase
KeywordsHYDROLASE / Chitinase / Hevein
Biological speciesSimarouba glauca (aceituno)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsKanalElamparithi, B. / Ramya, K.S. / Ankur, T. / Radha, A. / Gunasekaran, K.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India) India
CitationJournal: Int.J.Biol.Macromol. / Year: 2020
Title: Structure of intact chitinase with hevein domain from the plant Simarouba glauca, known for its traditional anti-inflammatory efficacy.
Authors: Balu, K.E. / Ramya, K.S. / Radha, A. / Krishnasamy, G.
History
DepositionJan 1, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Class-1 chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0258
Polymers31,6151
Non-polymers1,4107
Water7,224401
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint8 kcal/mol
Surface area13510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.811, 84.811, 100.536
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-512-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Class-1 chitinase


Mass: 31614.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Simarouba glauca (aceituno)

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Sugars , 2 types, 2 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(3-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 830.786 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4[DGlcpNAcb3-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+3)][b-D-GlcpNAc]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 406 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 401 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.28 Å3/Da / Density % sol: 62.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100mM Tris (pH-8.5), 200mM Magnesium Chloride and 20%PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 21, 2019 / Details: Cilindrical Mirror with 50 nm Pt-coating
RadiationMonochromator: Double Crystal Si111 with LN2 closed loop cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.659→41.482 Å / Num. obs: 49928 / % possible obs: 99.9 % / Redundancy: 6.69 % / Biso Wilson estimate: 18.87 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.076 / Net I/σ(I): 25.5
Reflection shellResolution: 1.66→1.7 Å / Mean I/σ(I) obs: 2.35 / Num. unique obs: 7006 / CC1/2: 0.776 / Rrim(I) all: 0.779 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MST

4mst


Resolution: 1.66→36.72 Å / SU ML: 0.1772 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.8709
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1927 1987 3.98 %
Rwork0.1733 47937 -
obs0.1741 49924 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.39 Å2
Refinement stepCycle: LAST / Resolution: 1.66→36.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2212 0 89 401 2702
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01892411
X-RAY DIFFRACTIONf_angle_d1.38883284
X-RAY DIFFRACTIONf_chiral_restr0.0942331
X-RAY DIFFRACTIONf_plane_restr0.0109447
X-RAY DIFFRACTIONf_dihedral_angle_d10.1173367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.70.25711400.23913357X-RAY DIFFRACTION98.67
1.7-1.750.26591360.21773366X-RAY DIFFRACTION100
1.75-1.80.24361440.18983410X-RAY DIFFRACTION100
1.8-1.860.19711380.18233355X-RAY DIFFRACTION100
1.86-1.920.23231410.1883407X-RAY DIFFRACTION100
1.92-20.21571450.18353409X-RAY DIFFRACTION100
2-2.090.19131360.18423388X-RAY DIFFRACTION100
2.09-2.20.18821430.17623396X-RAY DIFFRACTION100
2.2-2.340.18741390.16763431X-RAY DIFFRACTION100
2.34-2.520.20631450.17373408X-RAY DIFFRACTION100
2.52-2.770.18121430.16923451X-RAY DIFFRACTION100
2.77-3.170.20921420.17873440X-RAY DIFFRACTION100
3.17-40.17981450.16013484X-RAY DIFFRACTION100
4-36.720.16231500.15943635X-RAY DIFFRACTION99.95

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