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- PDB-2psp: Porcine pancreatic spasmolytic polypeptide -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2psp
TitlePorcine pancreatic spasmolytic polypeptide
ComponentsPORCINE PANCREATIC SPASMOLYTIC POLYPEPTIDE
KeywordsSIGNALING PROTEIN / GROWTH FACTOR / TREFOIL FAMILY OF PEPTIDES
Function / homology
Function and homology information


CXCR4 chemokine receptor binding / negative regulation of gastric acid secretion / maintenance of gastrointestinal epithelium / chemokine-mediated signaling pathway / growth factor activity / extracellular space
Similarity search - Function
P-type trefoil, chordata / Spasmolytic Protein, domain 1 / Spasmolytic Protein; domain 1 / P-type trefoil, conserved site / P-type 'Trefoil' domain signature. / Trefoil (P-type) domain / P-type trefoil domain / P-type trefoil domain superfamily / P-type 'Trefoil' domain profile. / P or trefoil or TFF domain ...P-type trefoil, chordata / Spasmolytic Protein, domain 1 / Spasmolytic Protein; domain 1 / P-type trefoil, conserved site / P-type 'Trefoil' domain signature. / Trefoil (P-type) domain / P-type trefoil domain / P-type trefoil domain superfamily / P-type 'Trefoil' domain profile. / P or trefoil or TFF domain / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 1.95 Å
AuthorsPetersen, T.N. / Henriksen, A. / Gajhede, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Structure of porcine pancreatic spasmolytic polypeptide at 1.95 A resolution.
Authors: Petersen, T.N. / Henriksen, A. / Gajhede, M.
#1: Journal: Structure / Year: 1993
Title: Pancreatic Spasmolytic Polypeptide: First Three-Dimensional Structure of a Member of the Mammalian Trefoil Family of Peptides
Authors: Gajhede, M. / Petersen, T.N. / Henriksen, A. / Petersen, J.F. / Dauter, Z. / Wilson, K.S. / Thim, L.
History
DepositionFeb 1, 1996Processing site: BNL
Revision 1.0Jul 11, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PORCINE PANCREATIC SPASMOLYTIC POLYPEPTIDE
B: PORCINE PANCREATIC SPASMOLYTIC POLYPEPTIDE


Theoretical massNumber of molelcules
Total (without water)23,4712
Polymers23,4712
Non-polymers00
Water3,297183
1
A: PORCINE PANCREATIC SPASMOLYTIC POLYPEPTIDE


Theoretical massNumber of molelcules
Total (without water)11,7351
Polymers11,7351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PORCINE PANCREATIC SPASMOLYTIC POLYPEPTIDE


Theoretical massNumber of molelcules
Total (without water)11,7351
Polymers11,7351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.600, 60.600, 113.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein PORCINE PANCREATIC SPASMOLYTIC POLYPEPTIDE / PSP


Mass: 11735.303 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P01359
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 52 %
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
22.0 M1reservoir(NH4)2SO4
37 %(w/v)PEG4001reservoir
40.1 MHEPES1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 15652 / % possible obs: 87.3 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.058

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Processing

Software
NameVersionClassification
DENZOdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 1.95→50 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.258 -10 %
Rwork0.198 --
obs0.198 15652 87.3 %
Displacement parametersBiso mean: 24.6 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1624 0 0 183 1807
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.685
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.76
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.635
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.76
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.635

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