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- PDB-6vj0: Crystal structure of a chitin-binding protein from Moringa oleife... -

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Basic information

Entry
Database: PDB / ID: 6vj0
TitleCrystal structure of a chitin-binding protein from Moringa oleifera seeds (Mo-CBP4)
ComponentsChitin-binding protein Mo-CBP4
KeywordsPLANT PROTEIN / Chitin-binding / Moringa oleifera / lectin
Function / homologyNapin/ 2S seed storage protein/Conglutin / Protease inhibitor/seed storage/LTP family / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / nutrient reservoir activity / ACETATE ION / 2S albumin
Function and homology information
Biological speciesMoringa oleifera (horseradish tree)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBezerra, E.H.S. / Lopes, T.D.P. / da Silva, F.M.S. / Costa, H.P.S. / Freire, V.N. / Rocha, B.A.M. / Sousa, D.O.B.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Coordination for the Improvement of Higher Education Personnel Brazil
CitationJournal: To Be Published
Title: Structural characterization of a lectin from Moringa oleifera seeds with imflammatory activities
Authors: Lopes, T.D.P. / Costa, H.P.S. / Pereira, M.L. / Neto, J.X.S. / de Alencar, N.M.N. / Vasconcelos, I.M. / Oliveira, J.T.A. / da Silva, F.M.S. / Freire, V.N. / Bezerra, E.H.S. / Rocha, B.A.M. / Sousa, D.O.B.
History
DepositionJan 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitin-binding protein Mo-CBP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4774
Polymers14,3471
Non-polymers1303
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.052, 107.052, 42.958
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-313-

HOH

21A-316-

HOH

31A-326-

HOH

41A-335-

HOH

51A-337-

HOH

61A-349-

HOH

71A-355-

HOH

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Components

#1: Protein Chitin-binding protein Mo-CBP4


Mass: 14347.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Moringa oleifera (horseradish tree) / References: UniProt: W5S2D2*PLUS
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.14 Å3/Da / Density % sol: 42.65 % / Description: rectangular-shaped crystals
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2.0 M Sodium chloride, 0.1 M Sodium acetate trihydrate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45 Å / Relative weight: 1
ReflectionResolution: 1.9→39.87 Å / Num. obs: 10152 / % possible obs: 100 % / Redundancy: 24.6 % / Biso Wilson estimate: 33.9 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.021 / Net I/σ(I): 32
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.688 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 641 / CC1/2: 0.86 / Rpim(I) all: 0.485 / % possible all: 100

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.25data extraction
PHENIX1.13refinement
PHASERphasing
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DOM

5dom


Resolution: 1.9→39.87 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.227 --
Rwork0.198 --
obs-10152 100 %
Displacement parametersBiso max: 95.31 Å2 / Biso mean: 41.6543 Å2 / Biso min: 13.84 Å2
Refinement stepCycle: LAST / Resolution: 1.9→39.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms728 0 6 55 789

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