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- PDB-7vs6: Phloem lectin (PP2) structure -native form -

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Basic information

Entry
Database: PDB / ID: 7vs6
TitlePhloem lectin (PP2) structure -native form
Components17 kDa phloem lectin
KeywordsSUGAR BINDING PROTEIN / Phloem lectin / chitin-binding lectin
Function / homologyPhloem protein 2-like / Phloem protein 2 / carbohydrate binding / : / 17 kDa phloem lectin
Function and homology information
Biological speciesCucumis sativus (cucumber)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 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
DepositionOct 25, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 17 kDa phloem lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8352
Polymers17,6401
Non-polymers1951
Water1,15364
1
A: 17 kDa phloem lectin
hetero molecules

A: 17 kDa phloem lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6704
Polymers35,2802
Non-polymers3902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+5/61
Buried area2600 Å2
ΔGint-58 kcal/mol
Surface area12860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.690, 52.690, 261.830
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein 17 kDa phloem lectin


Mass: 17639.871 Da / Num. of mol.: 1
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: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pt / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
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: 2.97 Å3/Da / Density % sol: 58.64 %
Crystal growTemperature: 295 K / Method: microbatch
Details: 1.0 M Ammonium citrate dibasic, 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: ELETTRA / Beamline: 11.2C / Wavelength: 1.5 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.5→45.6 Å / Num. obs: 575252 / % possible obs: 99.9 % / Redundancy: 70.1 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 56.6
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.198 / Num. unique obs: 8209

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
iMOSFLMdata reduction
SCALAdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→45.5 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.877 / Cross valid method: THROUGHOUT / ESU R: 0.335 / ESU R Free: 0.261
Details: HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.256 411 5.007 %
Rwork0.196 --
obs-8208 99.7 %
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: 18.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.685 Å20.343 Å20 Å2
2--0.685 Å20 Å2
3----2.223 Å2
Refinement stepCycle: LAST / Resolution: 2.5→45.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1187 0 1 64 1252
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131224
X-RAY DIFFRACTIONr_bond_other_d0.0360.0171067
X-RAY DIFFRACTIONr_angle_refined_deg1.741.6241670
X-RAY DIFFRACTIONr_angle_other_deg2.4791.5692460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9375146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.26222.12166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.36115183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.166157
X-RAY DIFFRACTIONr_chiral_restr0.1040.2158
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021378
X-RAY DIFFRACTIONr_gen_planes_other0.010.02291
X-RAY DIFFRACTIONr_nbd_refined0.1630.2173
X-RAY DIFFRACTIONr_nbd_other0.2140.234
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2543
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.254
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6431.951590
X-RAY DIFFRACTIONr_mcbond_other1.6441.951589
X-RAY DIFFRACTIONr_mcangle_it2.632.908734
X-RAY DIFFRACTIONr_mcangle_other2.6292.909735
X-RAY DIFFRACTIONr_scbond_it1.7782.048632
X-RAY DIFFRACTIONr_scbond_other1.7772.048633
X-RAY DIFFRACTIONr_scangle_it2.7893.019935
X-RAY DIFFRACTIONr_scangle_other2.7883.02936
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.57 Å
RfactorNum. reflection% reflection
Rfree0.235 34 -
Rwork0.156 539 -
obs--99.31 %

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