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- PDB-7vub: Phloem lectin (PP2) complex with Nitrobenzene -

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Basic information

Entry
Database: PDB / ID: 7vub
TitlePhloem lectin (PP2) complex with Nitrobenzene
ComponentsPhloem lectin
KeywordsSUGAR BINDING PROTEIN / Phloem lectin / chitin-binding lectin / Nitrobenzene complex
Function / homology: / Phloem protein 2-like / Phloem protein 2 / carbohydrate binding / NITROBENZENE / 17 kDa phloem lectin
Function and homology information
Biological speciesCucumis sativus (cucumber)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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 2, 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 9, 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

Downloads & links

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Assembly

Deposited unit
A: Phloem lectin
B: Phloem lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4654
Polymers35,2802
Non-polymers1852
Water6,521362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-10 kcal/mol
Surface area12770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.810, 70.470, 101.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phloem lectin / PP2


Mass: 17639.871 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: Chemical ChemComp-NBZ / NITROBENZENE


Mass: 123.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#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.: 362 / 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: 2.21 Å3/Da / Density % sol: 44.46 %
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 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→50.97 Å / Num. obs: 2585878 / % possible obs: 100 % / Redundancy: 26.6 % / Biso Wilson estimate: 11.7 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.073 / Net I/σ(I): 2.5
Reflection shellResolution: 1.2→1.22 Å / Rmerge(I) obs: 1.27 / Num. unique obs: 89698 / CC1/2: 0.85

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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: 1.2→50.9 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.04
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1893 4765 4.907 %
Rwork0.1603 92334 -
all0.162 --
obs-97099 99.971 %
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: 16.129 Å2
Baniso -1Baniso -2Baniso -3
1--2.676 Å2-0 Å20 Å2
2--1.756 Å2-0 Å2
3---0.92 Å2
Refinement stepCycle: LAST / Resolution: 1.2→50.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2413 0 13 362 2788
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0132499
X-RAY DIFFRACTIONr_bond_other_d0.0360.0172208
X-RAY DIFFRACTIONr_angle_refined_deg2.0261.6263401
X-RAY DIFFRACTIONr_angle_other_deg2.4011.5725093
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2255295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.48421.765136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.03215387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0291516
X-RAY DIFFRACTIONr_chiral_restr0.1130.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.022800
X-RAY DIFFRACTIONr_gen_planes_other0.0370.02600
X-RAY DIFFRACTIONr_nbd_refined0.1850.2328
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2210.21969
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21161
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.21158
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.2194
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0440.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.170.27
X-RAY DIFFRACTIONr_nbd_other0.1280.230
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1970.210
X-RAY DIFFRACTIONr_mcbond_it2.8441.4231189
X-RAY DIFFRACTIONr_mcbond_other2.8411.4221188
X-RAY DIFFRACTIONr_mcangle_it3.0362.1371481
X-RAY DIFFRACTIONr_mcangle_other3.0352.1381482
X-RAY DIFFRACTIONr_scbond_it5.0081.7171310
X-RAY DIFFRACTIONr_scbond_other5.011.7181311
X-RAY DIFFRACTIONr_scangle_it4.3382.4651920
X-RAY DIFFRACTIONr_scangle_other4.3362.4651921
X-RAY DIFFRACTIONr_lrange_it3.95529.19810436
X-RAY DIFFRACTIONr_lrange_other3.91429.06610399
X-RAY DIFFRACTIONr_rigid_bond_restr29.72834707
X-RAY DIFFRACTIONr_ncsr_local_group_10.0930.054609
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.2310.2463700.2126736X-RAY DIFFRACTION99.8595
1.231-1.2650.2593270.1996565X-RAY DIFFRACTION99.913
1.265-1.3020.2243340.1866407X-RAY DIFFRACTION99.9259
1.302-1.3420.2133450.1676193X-RAY DIFFRACTION100
1.342-1.3860.2053020.1676036X-RAY DIFFRACTION99.9369
1.386-1.4340.1923140.1545833X-RAY DIFFRACTION100
1.434-1.4880.1863060.1455631X-RAY DIFFRACTION99.9832
1.488-1.5490.1742810.1345434X-RAY DIFFRACTION100
1.549-1.6180.1632790.1245216X-RAY DIFFRACTION100
1.618-1.6970.1852480.1335010X-RAY DIFFRACTION100
1.697-1.7880.1752390.1394786X-RAY DIFFRACTION100
1.788-1.8970.1692040.144529X-RAY DIFFRACTION100
1.897-2.0280.1632280.1464251X-RAY DIFFRACTION100
2.028-2.190.1742200.1563965X-RAY DIFFRACTION100
2.19-2.3980.1751990.1463672X-RAY DIFFRACTION100
2.398-2.6810.1611490.1573365X-RAY DIFFRACTION100
2.681-3.0950.2231480.172974X-RAY DIFFRACTION100
3.095-3.7870.1991140.1732540X-RAY DIFFRACTION100
3.787-5.3450.16890.1652021X-RAY DIFFRACTION100
5.345-50.90.282690.2291171X-RAY DIFFRACTION99.839

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