[English] 日本語
Yorodumi
- PDB-1pos: CRYSTAL STRUCTURE OF A NOVEL DISULFIDE-LINKED "TREFOIL" MOTIF FOU... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pos
TitleCRYSTAL STRUCTURE OF A NOVEL DISULFIDE-LINKED "TREFOIL" MOTIF FOUND IN A LARGE FAMILY OF PUTATIVE GROWTH FACTORS
ComponentsPORCINE PANCREATIC SPASMOLYTIC POLYPEPTIDE
KeywordsGROWTH FACTOR
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 / 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
Similarity search - Domain/homology
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsDe, A. / Brown, D. / Gorman, M. / Carr, M. / Sanderson, M.R. / Freemont, P.S.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Crystal structure of a disulfide-linked "trefoil" motif found in a large family of putative growth factors.
Authors: De, A. / Brown, D.G. / Gorman, M.A. / Carr, M. / Sanderson, M.R. / Freemont, P.S.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: Crystallization and Preliminary X-Ray Diffraction Studies of Pancreatic Spasmolytic Polypeptide
Authors: Gorman, M.A. / De, A. / Freemont, P.S.
History
DepositionOct 8, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_ref_seq_dif.details
Revision 2.1Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
1
A: PORCINE PANCREATIC SPASMOLYTIC POLYPEPTIDE


Theoretical massNumber of molelcules
Total (without water)11,7351
Polymers11,7351
Non-polymers00
Water0
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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)181.680, 54.690, 72.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

-
Components

#1: Protein PORCINE PANCREATIC SPASMOLYTIC POLYPEPTIDE / Coordinate model: Cα atoms only


Mass: 11735.303 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P01359
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.85 Å3/Da / Density % sol: 68.03 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlpeptide1drop
210 mMHEPES1drop
314 %satammonium sulfate1reservoir
40.1 Msodium acetate1reservoir

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.6 Å / Num. obs: 10739 / % possible obs: 89.9 % / Rmerge(I) obs: 0.08

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.219 / Rfactor obs: 0.219 / Highest resolution: 2.6 Å
Refinement stepCycle: LAST / Highest resolution: 2.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms212 0 0 0 212
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Rfactor obs: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.6

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more