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- PDB-3r50: Structure analysis of a wound-inducible lectin ipomoelin from swe... -

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Basic information

Entry
Database: PDB / ID: 3r50
TitleStructure analysis of a wound-inducible lectin ipomoelin from sweet potato
ComponentsIpomoelin
KeywordsCarbohydrate-binding protein / beta prism / Carbohydrate/Sugar Binding
Function / homology
Function and homology information


defense response to insect / positive regulation of stress-activated MAPK cascade / response to wounding / carbohydrate binding / protein homotetramerization
Similarity search - Function
Jacalin-like lectin domain, plant / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain superfamily / Mainly Beta
Similarity search - Domain/homology
Biological speciesIpomoea batatas (sweet potato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsLiu, K.L. / Chang, W.C. / Jeng, S.T. / Cheng, Y.S.
CitationJournal: Plos One / Year: 2012
Title: Ipomoelin, a jacalin-related lectin with a compact tetrameric association and versatile carbohydrate binding properties regulated by its N terminus.
Authors: Chang, W.C. / Liu, K.L. / Hsu, F.C. / Jeng, S.T. / Cheng, Y.S.
History
DepositionMar 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2012Group: Database references
Revision 1.2Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ipomoelin
B: Ipomoelin
C: Ipomoelin
D: Ipomoelin
E: Ipomoelin


Theoretical massNumber of molelcules
Total (without water)86,7275
Polymers86,7275
Non-polymers00
Water6,666370
1
A: Ipomoelin
B: Ipomoelin
C: Ipomoelin
D: Ipomoelin


Theoretical massNumber of molelcules
Total (without water)69,3824
Polymers69,3824
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10530 Å2
ΔGint-28 kcal/mol
Surface area22220 Å2
MethodPISA
2
E: Ipomoelin

E: Ipomoelin

E: Ipomoelin

E: Ipomoelin


Theoretical massNumber of molelcules
Total (without water)69,3824
Polymers69,3824
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area9250 Å2
ΔGint-18 kcal/mol
Surface area22440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.486, 139.468, 189.873
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein
Ipomoelin


Mass: 17345.420 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ipomoea batatas (sweet potato) / Gene: ipomoelin / Plasmid: pTZ18UH-IPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P93193
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O

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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: 3.34 Å3/Da / Density % sol: 63.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.005 M ferric chloride, 0.05 M sodium citrate, 5% jeffamine M-600 against a reservoir of 0.01 M ferric chloride, 0.1 M sodium citrate, 10% jeffamine M-600, pH 5.6, VAPOR DIFFUSION, HANGING ...Details: 0.005 M ferric chloride, 0.05 M sodium citrate, 5% jeffamine M-600 against a reservoir of 0.01 M ferric chloride, 0.1 M sodium citrate, 10% jeffamine M-600, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 6, 2009 / Details: mirrors
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.27→30 Å / Num. obs: 51599 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 18.8
Reflection shellResolution: 2.27→2.35 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 4.65 / Num. unique all: 5264 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OUW

1ouw


Resolution: 2.27→26.21 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 344672.22 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 2472 5 %RANDOM
Rwork0.202 ---
obs0.202 49217 91.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.1792 Å2 / ksol: 0.279667 e/Å3
Displacement parametersBiso mean: 36.1 Å2
Baniso -1Baniso -2Baniso -3
1--6.05 Å20 Å20 Å2
2---4.16 Å20 Å2
3---10.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.27→26.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5794 0 0 370 6164
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.631.5
X-RAY DIFFRACTIONc_mcangle_it2.752
X-RAY DIFFRACTIONc_scbond_it2.142
X-RAY DIFFRACTIONc_scangle_it3.072.5
LS refinement shellResolution: 2.27→2.41 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.289 361 5 %
Rwork0.238 6886 -
obs--81.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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