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- PDB-5yrm: PPL3C-isomaltose complex -

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Basic information

Entry
Database: PDB / ID: 5yrm
TitlePPL3C-isomaltose complex
ComponentsPPL3-b
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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_poly / 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 / _entity_poly.pdbx_seq_one_letter_code_can / _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 2.1Nov 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 2.2Oct 23, 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: PPL3-b
B: PPL3-b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1687
Polymers31,4422
Non-polymers7275
Water8,665481
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-46 kcal/mol
Surface area12840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.350, 74.400, 90.540
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-b


Mass: 15720.907 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pteria penguin (invertebrata) / References: UniProt: A0A2Z5V8U8*PLUS
#2: Polysaccharide alpha-D-glucopyranose-(1-6)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
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
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 481 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsFor PPL3-b, the genebank assession is LC334154.1.

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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: 43.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium sulfate 25% (w/v) PEG 3350 0.1 M bis-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: 44601 / % possible obs: 100 % / Redundancy: 2 % / Rmerge(I) obs: 0.016 / Net I/σ(I): 24.3
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 2 % / Rmerge(I) obs: 0.075 / Mean I/σ(I) obs: 9.5 / Num. unique obs: 6404 / % possible all: 100

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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→19.741 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.73
RfactorNum. reflection% reflection
Rfree0.1939 2178 4.97 %
Rwork0.1656 --
obs0.167 43862 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→19.741 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2195 0 43 481 2719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112328
X-RAY DIFFRACTIONf_angle_d1.2163161
X-RAY DIFFRACTIONf_dihedral_angle_d17.452873
X-RAY DIFFRACTIONf_chiral_restr0.394348
X-RAY DIFFRACTIONf_plane_restr0.007393
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.499-1.53160.29491390.27812469X-RAY DIFFRACTION95
1.5316-1.56720.29581180.24922531X-RAY DIFFRACTION96
1.5672-1.60640.25751170.23912519X-RAY DIFFRACTION97
1.6064-1.64980.25611280.22282554X-RAY DIFFRACTION98
1.6498-1.69830.24821410.21452552X-RAY DIFFRACTION98
1.6983-1.75310.24621410.19532573X-RAY DIFFRACTION98
1.7531-1.81570.22241560.18622532X-RAY DIFFRACTION98
1.8157-1.88830.22811380.17562583X-RAY DIFFRACTION99
1.8883-1.97420.23711310.16772613X-RAY DIFFRACTION99
1.9742-2.07820.22621340.16172604X-RAY DIFFRACTION99
2.0782-2.20820.15521350.14332644X-RAY DIFFRACTION100
2.2082-2.37850.15311430.1432638X-RAY DIFFRACTION100
2.3785-2.61730.19681470.15522633X-RAY DIFFRACTION100
2.6173-2.99490.16191410.15032665X-RAY DIFFRACTION100
2.9949-3.7690.18271440.14252714X-RAY DIFFRACTION100
3.769-19.74270.15531250.15812860X-RAY DIFFRACTION100

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