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- PDB-5yre: Crystal structure of PPL3A -

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Basic information

Entry
Database: PDB / ID: 5yre
TitleCrystal structure of PPL3A
Components(PPL3-A) x 2
KeywordsSUGAR BINDING PROTEIN / Lectin / Biomineralization / Post-translational modification / Calcite / Docking simulation
Function / homologyJacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Jacalin-like lectin domain superfamily / carbohydrate binding / Jacalin-related lectin
Function and homology information
Biological speciesPteria penguin (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsNakae, S. / Shionyu, M. / Ogawa, T. / Shirai, T.
Funding support Japan, 4items
OrganizationGrant numberCountry
MEXTJP17H01818 Japan
AMED17am0101069j0001 Japan
MEXT#25107703 Japan
MEXT#23107505 Japan
CitationJournal: Proteins / Year: 2018
Title: Structures of jacalin-related lectin PPL3 regulating pearl shell biomineralization
Authors: Nakae, S. / Shionyu, M. / Ogawa, T. / Shirai, T.
History
DepositionNov 9, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 2.0Jan 1, 2020Group: Database references / Derived calculations ...Database references / Derived calculations / Polymer sequence / Structure summary
Category: entity / entity_poly ...entity / entity_poly / pdbx_struct_mod_residue / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PPL3-A
B: PPL3-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,33411
Polymers31,4782
Non-polymers8579
Water7,530418
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-61 kcal/mol
Surface area13380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.180, 50.210, 107.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PPL3-A


Mass: 15754.878 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pteria penguin (invertebrata) / References: UniProt: B6F0T7
#2: Protein PPL3-A


Mass: 15722.835 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pteria penguin (invertebrata) / References: UniProt: B6F0T7
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 418 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe N-terminus of subunit after signal peptide removal is Gln20-Val21 from mRNA, but is changed to ...The N-terminus of subunit after signal peptide removal is Gln20-Val21 from mRNA, but is changed to pGlu20-Val21 or Gln20-Ile21 because of post-translational modifications. The genebank accession for PPL3-a is AB425240.2.

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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: 1.93 Å3/Da / Density % sol: 36.4 %
Crystal growTemperature: 293 K / Method: small tubes
Details: 0.2M ammonium sulfate, 25%(w/v) PEG 3350, 0.1M Tris/bis-Tris buffer pH 5.5 microgravity environments on ISS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→20 Å / Num. obs: 44177 / % possible obs: 90.3 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.016 / Net I/σ(I): 27.1
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.148 / Mean I/σ(I) obs: 5.2 / Num. unique obs: 5714 / % possible all: 81.4

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YRK

5yrk


Resolution: 1.4→19.739 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.72
RfactorNum. reflection% reflection
Rfree0.2144 2216 5.04 %
Rwork0.1755 --
obs0.1774 43998 89.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.4→19.739 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2212 0 47 418 2677
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092344
X-RAY DIFFRACTIONf_angle_d1.093179
X-RAY DIFFRACTIONf_dihedral_angle_d16.735868
X-RAY DIFFRACTIONf_chiral_restr0.083337
X-RAY DIFFRACTIONf_plane_restr0.006396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.43040.37871200.32582256X-RAY DIFFRACTION79
1.4304-1.46370.33851270.28562317X-RAY DIFFRACTION81
1.4637-1.50030.31381470.26362282X-RAY DIFFRACTION80
1.5003-1.54080.29571040.23672330X-RAY DIFFRACTION81
1.5408-1.58620.25311220.21732318X-RAY DIFFRACTION81
1.5862-1.63730.24281210.20952340X-RAY DIFFRACTION81
1.6373-1.69580.23991180.19232384X-RAY DIFFRACTION83
1.6958-1.76370.22731530.19122447X-RAY DIFFRACTION86
1.7637-1.84390.25441430.182596X-RAY DIFFRACTION91
1.8439-1.9410.20761480.17562806X-RAY DIFFRACTION96
1.941-2.06250.21021680.16062829X-RAY DIFFRACTION99
2.0625-2.22160.20051440.1542905X-RAY DIFFRACTION100
2.2216-2.44480.18221450.16132938X-RAY DIFFRACTION100
2.4448-2.79770.22771310.17512962X-RAY DIFFRACTION100
2.7977-3.52150.20371500.15552988X-RAY DIFFRACTION100
3.5215-19.74130.17751750.16023084X-RAY DIFFRACTION100

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