[English] 日本語
Yorodumi
- PDB-1plf: THE THREE-DIMENSIONAL STRUCTURE OF BOVINE PLATELET FACTOR 4 AT 3.... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1plf
TitleTHE THREE-DIMENSIONAL STRUCTURE OF BOVINE PLATELET FACTOR 4 AT 3.0 ANGSTROMS RESOLUTION
ComponentsPLATELET FACTOR 4
KeywordsPLATELET FACTOR
Function / homology
Function and homology information


CXCR3 chemokine receptor binding / CXCR chemokine receptor binding / chemokine-mediated signaling pathway / leukocyte chemotaxis / chemokine activity / negative regulation of megakaryocyte differentiation / neutrophil chemotaxis / negative regulation of angiogenesis / adenylate cyclase-activating G protein-coupled receptor signaling pathway / platelet activation ...CXCR3 chemokine receptor binding / CXCR chemokine receptor binding / chemokine-mediated signaling pathway / leukocyte chemotaxis / chemokine activity / negative regulation of megakaryocyte differentiation / neutrophil chemotaxis / negative regulation of angiogenesis / adenylate cyclase-activating G protein-coupled receptor signaling pathway / platelet activation / cytokine-mediated signaling pathway / antimicrobial humoral immune response mediated by antimicrobial peptide / heparin binding / regulation of cell population proliferation / cellular response to lipopolysaccharide / inflammatory response / immune response / positive regulation of transcription by RNA polymerase II / extracellular space
Similarity search - Function
Platelet factor 4 / CXC chemokine / CXC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-x-C subfamily signature. / CXC Chemokine domain / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 ...Platelet factor 4 / CXC chemokine / CXC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-x-C subfamily signature. / CXC Chemokine domain / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
TETRACYANONICKELATE ION / Platelet factor 4
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsSt Charles, R. / Edwards, B.F.P.
Citation
Journal: J.Biol.Chem. / Year: 1989
Title: The three-dimensional structure of bovine platelet factor 4 at 3.0-A resolution.
Authors: St Charles, R. / Walz, D.A. / Edwards, B.F.
#1: Journal: J.Mol.Biol. / Year: 1984
Title: X-Ray Diffraction Analysis of Crystals of Bovine Platelet Factor 4
Authors: Charles, R.St. / Ciaglowski, R.E. / Walz, D. / Edwards, B.F.P.
History
DepositionOct 20, 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 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PLATELET FACTOR 4
B: PLATELET FACTOR 4
C: PLATELET FACTOR 4
D: PLATELET FACTOR 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7035
Polymers31,5414
Non-polymers1631
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-37 kcal/mol
Surface area13030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.700, 68.000, 80.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
PLATELET FACTOR 4


Mass: 7885.171 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P02777
#2: Chemical ChemComp-TCN / TETRACYANONICKELATE ION


Mass: 162.763 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4N4Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE FIRST THIRTEEN RESIDUES OF THE NATIVE PROTEIN WERE PROTEOLYTICALLY REMOVED WITH PORCINE ...THE FIRST THIRTEEN RESIDUES OF THE NATIVE PROTEIN WERE PROTEOLYTICALLY REMOVED WITH PORCINE ELASTASE PRIOR TO CRYSTALLIZATION. DENSITY WAS POOR OR LACKING FOR RESIDUES 14 - 22 IN MONOMERS 'A' AND 'C' AND FOR RESIDUES 14 - 20 IN MONOMERS 'B' AND 'D'. THESE REGIONS OF THE PROTEIN WERE NOT MODELED.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.36 %
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
20.4 M1dropNaCl
30.02-0.14 M1reservoirNaCl

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 10 Å / Num. all: 7080 / Num. measured all: 6901 / Rmerge(I) obs: 0.047

-
Processing

Software
NameClassification
X-PLORmodel building
PROFFTrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.2→10 Å / σ(F): 2
Details: THERE IS ONE NI(CN)4 (-2) ANION BOUND PER TETRAMER IN THE UNIT CELL. BINDING OF THIS COMPLEX WAS NECESSARY IN ORDER TO PREPARE A CRYSTAL FORM ISOMORPHOUS WITH A SINGLE PT(CN)4 DERIVATIVE ...Details: THERE IS ONE NI(CN)4 (-2) ANION BOUND PER TETRAMER IN THE UNIT CELL. BINDING OF THIS COMPLEX WAS NECESSARY IN ORDER TO PREPARE A CRYSTAL FORM ISOMORPHOUS WITH A SINGLE PT(CN)4 DERIVATIVE USED IN PHASING THE PARENT CRYSTAL DATA.
RfactorNum. reflection
Rwork0.209 -
obs0.209 14466
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1970 0 9 79 2058
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.019
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_deg
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_it1.3621
X-RAY DIFFRACTIONx_mcangle_it2.4891.5
X-RAY DIFFRACTIONx_scbond_it2.2191.5
X-RAY DIFFRACTIONx_scangle_it3.7472
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 10 Å / Num. reflection obs: 14466 / σ(F): 2 / Rfactor obs: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_angle_d0.030.046
X-RAY DIFFRACTIONx_planar_d0.050.064
X-RAY DIFFRACTIONx_plane_restr0.020.014
X-RAY DIFFRACTIONx_chiral_restr0.150.17

+
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://pdbjlvh1.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