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- PDB-5yrk: Crystal structure of PPL3C -

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Basic information

Entry
Database: PDB / ID: 5yrk
TitleCrystal structure of PPL3C
ComponentsPPL3-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
Function and homology information
Biological speciesPteria penguin (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.35 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

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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)32,21010
Polymers31,4422
Non-polymers7698
Water8,143452
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-93 kcal/mol
Surface area12990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.250, 73.790, 90.500
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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 452 / Source method: isolated from a natural source / Formula: H2O
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: 2.14 Å3/Da / Density % sol: 42.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2M ammonium sulfate, 25%(w/v) PEG3350, 0.1M bis-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: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→20 Å / Num. obs: 60077 / % possible obs: 100 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.018 / Net I/σ(I): 45
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.079 / Mean I/σ(I) obs: 10.2 / Num. unique obs: 8669 / % 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: SIRAS / Resolution: 1.35→19.723 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.22
RfactorNum. reflection% reflection
Rfree0.2058 2948 5.04 %
Rwork0.1792 --
obs0.1806 58493 97.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.35→19.723 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2192 0 40 452 2684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082357
X-RAY DIFFRACTIONf_angle_d1.1283208
X-RAY DIFFRACTIONf_dihedral_angle_d16.571887
X-RAY DIFFRACTIONf_chiral_restr0.403345
X-RAY DIFFRACTIONf_plane_restr0.007401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.37210.33531280.36822468X-RAY DIFFRACTION92
1.3721-1.39580.35071150.33832498X-RAY DIFFRACTION93
1.3958-1.42120.34691490.31792511X-RAY DIFFRACTION94
1.4212-1.44850.32691470.29652519X-RAY DIFFRACTION94
1.4485-1.47810.30081380.26542557X-RAY DIFFRACTION95
1.4781-1.51020.25911370.24812550X-RAY DIFFRACTION96
1.5102-1.54530.25291280.21652606X-RAY DIFFRACTION97
1.5453-1.58390.24891180.21432606X-RAY DIFFRACTION97
1.5839-1.62670.24891430.20352639X-RAY DIFFRACTION98
1.6267-1.67460.20861460.1972637X-RAY DIFFRACTION98
1.6746-1.72860.25031300.18382631X-RAY DIFFRACTION98
1.7286-1.79030.20381390.17922666X-RAY DIFFRACTION98
1.7903-1.8620.18921290.17692694X-RAY DIFFRACTION99
1.862-1.94660.20241250.16272702X-RAY DIFFRACTION99
1.9466-2.04920.19991350.16012708X-RAY DIFFRACTION99
2.0492-2.17740.20171460.14972692X-RAY DIFFRACTION100
2.1774-2.34530.15091520.1542714X-RAY DIFFRACTION100
2.3453-2.58080.17821570.16482731X-RAY DIFFRACTION100
2.5808-2.95320.21481510.16742740X-RAY DIFFRACTION100
2.9532-3.71670.17191660.14522768X-RAY DIFFRACTION100
3.7167-19.72480.18791690.16172908X-RAY DIFFRACTION100

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