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- PDB-5yrg: PPL3A-isomaltose complex -

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Basic information

Entry
Database: PDB / ID: 5yrg
TitlePPL3A-isomaltose complex
Components(PPL3-A) x 2
KeywordsSUGAR BINDING PROTEIN / Lectin / Biomineralization / Post-translational modification / Calcite / Docking simulation
Function / homologyJacalin-like lectin domain / Jacalin-type lectin domain profile. / Jacalin-like lectin domain / Jacalin-like lectin domain / 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: 1.5 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: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence / Structure summary
Category: chem_comp / entity ...chem_comp / entity / entity_poly / pdbx_struct_mod_residue / struct_ref_seq_dif
Item: _chem_comp.type / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code_can
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 3.2Nov 13, 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: PPL3-A
B: PPL3-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5478
Polymers31,4782
Non-polymers1,0696
Water7,350408
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-31 kcal/mol
Surface area13090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.950, 50.120, 118.090
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: Polysaccharide alpha-D-glucopyranose-(1-6)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(6+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 408 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsThe genebank accession for PPL3-a is AB425240.2. The N-terminus of subunit after signal peptide ...The genebank accession for PPL3-a is AB425240.2. 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: 2.16 Å3/Da / Density % sol: 43.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2M ammonium sulfate, 25%(w/v) PEG 3350, 0.1M Tris buffer pH 5.5

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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: 1.5→20 Å / Num. obs: 44443 / % possible obs: 99.7 % / Redundancy: 2 % / Rmerge(I) obs: 0.02 / Net I/σ(I): 17.6
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 2 % / Rmerge(I) obs: 0.113 / Mean I/σ(I) obs: 5.1 / Num. unique obs: 6432 / % possible all: 99.7

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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: 1.5→19.842 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.56
RfactorNum. reflection% reflection
Rfree0.2237 2116 4.84 %
Rwork0.1767 --
obs0.1789 43692 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→19.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2212 0 66 408 2686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012437
X-RAY DIFFRACTIONf_angle_d1.1453320
X-RAY DIFFRACTIONf_dihedral_angle_d16.01908
X-RAY DIFFRACTIONf_chiral_restr0.281370
X-RAY DIFFRACTIONf_plane_restr0.006411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.53490.37811220.33212633X-RAY DIFFRACTION94
1.5349-1.57330.37681410.28652674X-RAY DIFFRACTION97
1.5733-1.61580.29181410.26332710X-RAY DIFFRACTION97
1.6158-1.66330.31581280.24512711X-RAY DIFFRACTION97
1.6633-1.71690.25781350.22832714X-RAY DIFFRACTION98
1.7169-1.77830.28941340.21442734X-RAY DIFFRACTION98
1.7783-1.84940.27381390.20692735X-RAY DIFFRACTION98
1.8494-1.93350.22731340.19372767X-RAY DIFFRACTION98
1.9335-2.03540.23361330.17822770X-RAY DIFFRACTION99
2.0354-2.16280.21081380.17542802X-RAY DIFFRACTION99
2.1628-2.32950.23051530.16322787X-RAY DIFFRACTION99
2.3295-2.56350.23491560.16662808X-RAY DIFFRACTION99
2.5635-2.93340.211470.16422837X-RAY DIFFRACTION99
2.9334-3.69190.18081500.14522880X-RAY DIFFRACTION100
3.6919-19.84420.18991650.14843014X-RAY DIFFRACTION100

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