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- PDB-7vwb: Phloem lectin (PP2) structure -complex with N-Acetyllactosamine (... -

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Basic information

Entry
Database: PDB / ID: 7vwb
TitlePhloem lectin (PP2) structure -complex with N-Acetyllactosamine (LacNAc)
Componentsphloem lectin
KeywordsSUGAR BINDING PROTEIN / Phloem lectin / chitin-binding lectin
Function / homology: / Phloem protein 2-like / Phloem protein 2 / carbohydrate binding / N-acetyl-alpha-lactosamine / 17 kDa phloem lectin
Function and homology information
Biological speciesCucumis sativus (cucumber)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSivaji, N. / Bobbili, K.B. / Suguna, K. / Surolia, A.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
CitationJournal: Structure / Year: 2023
Title: Structure and interactions of the phloem lectin (phloem protein 2) Cus17 from Cucumis sativus.
Authors: Sivaji, N. / Bobbili, K.B. / Suguna, K. / Surolia, A.
History
DepositionNov 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 30, 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: phloem lectin
B: phloem lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1335
Polymers35,3042
Non-polymers8293
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint5 kcal/mol
Surface area12740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.690, 60.390, 82.980
Angle α, β, γ (deg.)90.000, 99.130, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein phloem lectin / PP2


Mass: 17651.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cucumis sativus (cucumber) / Gene: Lec17-7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8LK69
#2: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Glycan component / Mass: 383.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: N-acetyl-alpha-lactosamine
DescriptorTypeProgram
DGalpb1-4DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][<C8N1O3>]{[(1+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.67 Å3/Da / Density % sol: 53.95 %
Crystal growTemperature: 295 K / Method: microbatch
Details: 0.1 M MES monohydrate pH 6.0, 22% v/v Polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30.19 Å / Num. obs: 28551 / % possible obs: 98 % / Redundancy: 4 % / CC1/2: 0.97 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.18 / Num. unique obs: 4055 / CC1/2: 0.88

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VS6

7vs6


Resolution: 1.9→24.896 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.89 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.153
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2485 1468 5.142 %
Rwork0.2185 27080 -
all0.22 --
obs-28548 98.012 %
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: 13.985 Å2
Baniso -1Baniso -2Baniso -3
1-1.64 Å20 Å2-0.141 Å2
2---1.233 Å2-0 Å2
3----0.344 Å2
Refinement stepCycle: LAST / Resolution: 1.9→24.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2423 0 56 240 2719
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132555
X-RAY DIFFRACTIONr_bond_other_d0.0350.0182256
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.6543487
X-RAY DIFFRACTIONr_angle_other_deg2.351.6095206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.185298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.32921.241137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00215384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3311518
X-RAY DIFFRACTIONr_chiral_restr0.0730.2341
X-RAY DIFFRACTIONr_chiral_restr_other0.0210.26
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022820
X-RAY DIFFRACTIONr_gen_planes_other0.0150.02610
X-RAY DIFFRACTIONr_nbd_refined0.1830.2437
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2250.22226
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21185
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.21166
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2216
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0360.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2540.25
X-RAY DIFFRACTIONr_nbd_other0.3730.231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2510.28
X-RAY DIFFRACTIONr_mcbond_it1.1921.4141198
X-RAY DIFFRACTIONr_mcbond_other1.1891.4131197
X-RAY DIFFRACTIONr_mcangle_it1.8922.1161494
X-RAY DIFFRACTIONr_mcangle_other1.8932.1161495
X-RAY DIFFRACTIONr_scbond_it1.441.5221357
X-RAY DIFFRACTIONr_scbond_other1.4371.5221357
X-RAY DIFFRACTIONr_scangle_it2.2012.2421993
X-RAY DIFFRACTIONr_scangle_other2.2022.2431994
X-RAY DIFFRACTIONr_lrange_it4.38826.60410751
X-RAY DIFFRACTIONr_lrange_other4.38226.54510715
X-RAY DIFFRACTIONr_ncsr_local_group_10.0440.054970
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9490.3351290.2371893X-RAY DIFFRACTION95.8748
1.949-2.0030.2621100.2251922X-RAY DIFFRACTION96.7619
2.003-2.0610.258860.2181879X-RAY DIFFRACTION97.085
2.061-2.1240.262960.2211818X-RAY DIFFRACTION97.3055
2.124-2.1940.218770.2081813X-RAY DIFFRACTION97.6744
2.194-2.2710.239950.21682X-RAY DIFFRACTION97.5302
2.271-2.3560.2431020.1981684X-RAY DIFFRACTION97.9167
2.356-2.4520.262760.2181589X-RAY DIFFRACTION98.1143
2.452-2.5610.224770.2151547X-RAY DIFFRACTION98.3646
2.561-2.6860.274810.2231512X-RAY DIFFRACTION98.8827
2.686-2.8310.248790.2121377X-RAY DIFFRACTION98.7788
2.831-3.0030.261830.2181332X-RAY DIFFRACTION99.0896
3.003-3.210.253760.2231260X-RAY DIFFRACTION98.8897
3.21-3.4670.236610.2331178X-RAY DIFFRACTION99.5181
3.467-3.7970.274510.2361105X-RAY DIFFRACTION99.3127
3.797-4.2440.218590.202962X-RAY DIFFRACTION99.4158
4.244-4.8980.2360.195889X-RAY DIFFRACTION99.0364
4.898-5.9940.246560.235729X-RAY DIFFRACTION99.2415
5.994-8.4540.245260.259587X-RAY DIFFRACTION99.3517
8.454-240.214120.221322X-RAY DIFFRACTION94.0845

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