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- PDB-5yrf: PPL3A-trehalose complex -

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Basic information

Entry
Database: PDB / ID: 5yrf
TitlePPL3A-trehalose complex
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 / trehalose / alpha-D-glucopyranose / Jacalin-related lectin
Function and homology information
Biological speciesPteria penguin (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 / entity_name_com / 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_molecule_features / 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_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,5659
Polymers31,4782
Non-polymers1,0877
Water7,602422
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-50 kcal/mol
Surface area13210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.490, 50.440, 114.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#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

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Sugars , 2 types, 3 molecules

#3: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Sugar ChemComp-GLC / alpha-D-glucopyranose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 426 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 422 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.1 Å3/Da / Density % sol: 41.3 %
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: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 27993 / % possible obs: 94 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 11.8
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.122 / Mean I/σ(I) obs: 5.6 / Num. unique obs: 3966 / % possible all: 93.1

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→19.56 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.22
RfactorNum. reflection% reflection
Rfree0.2446 1398 5.02 %
Rwork0.1906 --
obs0.1934 27844 93.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→19.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2212 0 55 422 2689
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112331
X-RAY DIFFRACTIONf_angle_d1.153157
X-RAY DIFFRACTIONf_dihedral_angle_d15.498871
X-RAY DIFFRACTIONf_chiral_restr0.36345
X-RAY DIFFRACTIONf_plane_restr0.007390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.76070.33191390.25262527X-RAY DIFFRACTION92
1.7607-1.83120.32171290.23352584X-RAY DIFFRACTION92
1.8312-1.91440.25921370.21682576X-RAY DIFFRACTION92
1.9144-2.01530.28511370.19432583X-RAY DIFFRACTION92
2.0153-2.14140.24321290.19092598X-RAY DIFFRACTION93
2.1414-2.30650.24461430.1832604X-RAY DIFFRACTION92
2.3065-2.53820.25791400.19572595X-RAY DIFFRACTION92
2.5382-2.90440.23981270.20332612X-RAY DIFFRACTION92
2.9044-3.65540.26391390.17012763X-RAY DIFFRACTION96
3.6554-19.56170.19451780.17493004X-RAY DIFFRACTION100

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