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- PDB-5yjh: Structural insights into periostin functions -

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Basic information

Entry
Database: PDB / ID: 5yjh
TitleStructural insights into periostin functions
ComponentsPeriostin
KeywordsCELL ADHESION / tissue regeneration
Function / homology
Function and homology information


bone regeneration / cellular response to vitamin K / negative regulation of substrate adhesion-dependent cell spreading / regulation of Notch signaling pathway / tissue development / regulation of systemic arterial blood pressure / cellular response to fibroblast growth factor stimulus / positive regulation of chemokine (C-X-C motif) ligand 2 production / response to muscle activity / neuron projection extension ...bone regeneration / cellular response to vitamin K / negative regulation of substrate adhesion-dependent cell spreading / regulation of Notch signaling pathway / tissue development / regulation of systemic arterial blood pressure / cellular response to fibroblast growth factor stimulus / positive regulation of chemokine (C-X-C motif) ligand 2 production / response to muscle activity / neuron projection extension / negative regulation of cell-matrix adhesion / positive regulation of smooth muscle cell migration / response to mechanical stimulus / cell adhesion molecule binding / cellular response to transforming growth factor beta stimulus / extracellular matrix organization / extracellular matrix / macroautophagy / neuromuscular junction / trans-Golgi network / response to estradiol / cellular response to tumor necrosis factor / heparin binding / collagen-containing extracellular matrix / cell adhesion / response to hypoxia / extracellular space / metal ion binding
Similarity search - Function
TGF beta-induced protein/periostin / EMI domain / EMI domain profile. / FAS1 domain / FAS1 domain superfamily / Fasciclin domain / FAS1/BIgH3 domain profile. / Four repeated domains in the Fasciclin I family of proteins, present in many other contexts.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.957 Å
AuthorsLiu, H. / Liu, J. / Xu, F.
CitationJournal: FEBS Lett. / Year: 2018
Title: Structural characterizations of human periostin dimerization and cysteinylation.
Authors: Liu, J. / Zhang, J. / Xu, F. / Lin, Z. / Li, Z. / Liu, H.
History
DepositionOct 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Periostin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,64133
Polymers69,5761
Non-polymers1,06632
Water2,954164
1
A: Periostin
hetero molecules

A: Periostin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,28266
Polymers139,1512
Non-polymers2,13164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556x-y,-y,-z+11
Buried area10130 Å2
ΔGint-568 kcal/mol
Surface area54530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.529, 105.529, 330.342
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-960-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Periostin / PN / Osteoblast-specific factor 2 / OSF-2


Mass: 69575.641 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 22-631
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POSTN, OSF2 / Production host: Homo sapiens (human) / References: UniProt: Q15063

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Non-polymers , 6 types, 196 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O

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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: 3.92 Å3/Da / Density % sol: 68.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Ammonium Sulfate. Sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.957→50 Å / Num. obs: 22983 / % possible obs: 96.4 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.062 / Rrim(I) all: 0.131 / Rsym value: 0.089 / Χ2: 1.32 / Net I/σ(I): 14.1
Reflection shellResolution: 2.957→3.01 Å / Redundancy: 4 % / Rmerge(I) obs: 0.547 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1117 / CC1/2: 0.876 / Rpim(I) all: 0.295 / Rrim(I) all: 0.626 / Rsym value: 0.413 / Χ2: 1.046 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2LTB

2ltb


Resolution: 2.957→44.041 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.93
RfactorNum. reflection% reflection
Rfree0.2418 1146 5.01 %
Rwork0.2134 --
obs0.2148 22879 96.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.957→44.041 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4603 0 32 164 4799
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044692
X-RAY DIFFRACTIONf_angle_d0.616347
X-RAY DIFFRACTIONf_dihedral_angle_d17.1431773
X-RAY DIFFRACTIONf_chiral_restr0.049742
X-RAY DIFFRACTIONf_plane_restr0.004816
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9566-3.09110.35911330.29912662X-RAY DIFFRACTION96
3.0911-3.2540.28791240.2832668X-RAY DIFFRACTION97
3.254-3.45780.3071480.24912651X-RAY DIFFRACTION97
3.4578-3.72470.26811420.22852698X-RAY DIFFRACTION97
3.7247-4.09930.22851570.20692696X-RAY DIFFRACTION97
4.0993-4.69190.19731500.16852711X-RAY DIFFRACTION96
4.6919-5.9090.20931500.18952773X-RAY DIFFRACTION96
5.909-44.04590.22931420.20572874X-RAY DIFFRACTION93

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