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- PDB-5yrh: Crystal structure of PPL3B -

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Basic information

Entry
Database: PDB / ID: 5yrh
TitleCrystal structure of PPL3B
Components
  • PPL3-a
  • PPL3-b
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 / Jacalin-related lectin
Function and homology information
Biological speciesPteria penguin (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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 2.0Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Polymer sequence / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)31,9567
Polymers31,4762
Non-polymers4805
Water7,350408
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-47 kcal/mol
Surface area13380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.350, 50.440, 107.460
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-b


Mass: 15720.907 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pteria penguin (invertebrata) / References: UniProt: A0A2Z5V8U8*PLUS
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe genebank accession for PPL3-a is AB425240.2. For PPL3-b, the genebank assession is LC334154.1. ...The genebank accession for PPL3-a is AB425240.2. For PPL3-b, the genebank assession is LC334154.1. 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.

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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: 1.95 Å3/Da / Density % sol: 37 %
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: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→20 Å / Num. obs: 76214 / % possible obs: 98 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.009 / Net I/σ(I): 10
Reflection shellResolution: 1.2→1.26 Å / Redundancy: 2 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 7.2 / Num. unique obs: 11005 / % possible all: 98.1

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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: 1.2→19.772 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.22
RfactorNum. reflection% reflection
Rfree0.2248 3718 4.94 %
Rwork0.1914 --
obs0.193 75307 96.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.2→19.772 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2211 0 25 408 2644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012480
X-RAY DIFFRACTIONf_angle_d1.1833395
X-RAY DIFFRACTIONf_dihedral_angle_d18.551983
X-RAY DIFFRACTIONf_chiral_restr0.089364
X-RAY DIFFRACTIONf_plane_restr0.007428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.21520.37551390.36432572X-RAY DIFFRACTION96
1.2152-1.23120.34141430.35612536X-RAY DIFFRACTION94
1.2312-1.2480.38061540.34182547X-RAY DIFFRACTION96
1.248-1.26590.38491260.33052570X-RAY DIFFRACTION94
1.2659-1.28480.35711340.32912606X-RAY DIFFRACTION96
1.2848-1.30480.3381390.31442527X-RAY DIFFRACTION94
1.3048-1.32620.32821260.30622581X-RAY DIFFRACTION95
1.3262-1.34910.30331360.2852558X-RAY DIFFRACTION95
1.3491-1.37360.32981280.29512600X-RAY DIFFRACTION95
1.3736-1.40.33081190.27252586X-RAY DIFFRACTION95
1.4-1.42860.30421230.26012575X-RAY DIFFRACTION95
1.4286-1.45960.26421270.24792602X-RAY DIFFRACTION95
1.4596-1.49360.30091420.23342577X-RAY DIFFRACTION94
1.4936-1.53090.26751320.22572569X-RAY DIFFRACTION95
1.5309-1.57230.22771480.20892576X-RAY DIFFRACTION95
1.5723-1.61850.23851350.20642620X-RAY DIFFRACTION96
1.6185-1.67080.23531390.20212618X-RAY DIFFRACTION97
1.6708-1.73040.20351470.19112677X-RAY DIFFRACTION98
1.7304-1.79970.2031290.18882753X-RAY DIFFRACTION100
1.7997-1.88150.20141520.18472735X-RAY DIFFRACTION100
1.8815-1.98060.22761430.17362720X-RAY DIFFRACTION100
1.9806-2.10460.18621330.17212777X-RAY DIFFRACTION100
2.1046-2.26690.20151480.1622773X-RAY DIFFRACTION100
2.2669-2.49460.19161520.16362752X-RAY DIFFRACTION100
2.4946-2.85470.22211210.17262828X-RAY DIFFRACTION100
2.8547-3.59310.19521570.15172813X-RAY DIFFRACTION100
3.5931-19.77470.19461460.16222941X-RAY DIFFRACTION99

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