[English] 日本語
Yorodumi
- PDB-1f9p: CRYSTAL STRUCTURE OF CONNECTIVE TISSUE ACTIVATING PEPTIDE-III(CTA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1f9p
TitleCRYSTAL STRUCTURE OF CONNECTIVE TISSUE ACTIVATING PEPTIDE-III(CTAP-III) COMPLEXED WITH POLYVINYLSULFONIC ACID
ComponentsCONNECTIVE TISSUE ACTIVATING PEPTIDE-III
KeywordsBLOOD CLOTTING / chemokine-heparin analog complex
Function / homology
Function and homology information


glucose transmembrane transporter activity / glucose transmembrane transport / CXCR chemokine receptor binding / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / positive regulation of cell division / neutrophil chemotaxis / platelet alpha granule lumen / growth factor activity ...glucose transmembrane transporter activity / glucose transmembrane transport / CXCR chemokine receptor binding / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / positive regulation of cell division / neutrophil chemotaxis / platelet alpha granule lumen / growth factor activity / antimicrobial humoral immune response mediated by antimicrobial peptide / Platelet degranulation / tertiary granule lumen / G alpha (i) signalling events / cellular response to lipopolysaccharide / defense response to bacterium / inflammatory response / Neutrophil degranulation / extracellular space / extracellular region
Similarity search - Function
CXC chemokine / CXC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-x-C subfamily signature. / CXC Chemokine domain / Chemokine beta/gamma/delta / 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 ...CXC chemokine / CXC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-x-C subfamily signature. / CXC Chemokine domain / Chemokine beta/gamma/delta / 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
ETHANESULFONIC ACID / Platelet basic protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.93 Å
AuthorsYang, J. / Faulk, T. / Aster, R. / Visentin, G. / Edwards, B. / Castor, C.
CitationJournal: To be Published
Title: Structure of the CXC Chemokine, Connective Tissue Activating Peptide-III, Complexed with the Heparin Analogue, Polyvinylsulfonic Acid
Authors: Yang, J. / Faulk, T. / Aster, R. / Visentin, G. / Edwards, B. / Castor, C.
History
DepositionJul 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CONNECTIVE TISSUE ACTIVATING PEPTIDE-III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6384
Polymers9,3081
Non-polymers3303
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.700, 54.700, 58.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein CONNECTIVE TISSUE ACTIVATING PEPTIDE-III / CTAP-III


Mass: 9307.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: PLATELET BASIC PROTEIN N-TERMINAL TRUNCATION PRODUCT
Source: (natural) Homo sapiens (human) / Cell: PLATELETS / References: UniProt: P02775
#2: Chemical ChemComp-ESA / ETHANESULFONIC ACID / Ethanesulfonic acid


Mass: 110.132 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.47 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4
Details: PEG 1000, sodium acetate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. all: 7080 / Num. obs: 7080 / % possible obs: 99.6 % / Observed criterion σ(I): 1 / Redundancy: 15 % / Biso Wilson estimate: 41.9 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 47.8
Reflection shellResolution: 1.93→2 Å / Redundancy: 10 % / Num. unique all: 670 / % possible all: 97.5

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
EPMRphasing
CNS0.4refinement
RefinementResolution: 1.93→15 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 585333.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 735 10.9 %RANDOM
Rwork0.232 ---
obs0.232 6734 95.3 %-
all-6734 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 93.96 Å2 / ksol: 0.315 e/Å3
Displacement parametersBiso mean: 54.8 Å2
Baniso -1Baniso -2Baniso -3
1-3.84 Å20 Å20 Å2
2--3.84 Å20 Å2
3----7.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.26 Å
Luzzati d res low-15 Å
Luzzati sigma a0.31 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.93→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms618 0 18 133 769
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.99
X-RAY DIFFRACTIONc_mcbond_it1.581.5
X-RAY DIFFRACTIONc_mcangle_it2.722
X-RAY DIFFRACTIONc_scbond_it1.862
X-RAY DIFFRACTIONc_scangle_it3.022.5
LS refinement shellResolution: 1.93→2.05 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.402 95 10.4 %
Rwork0.378 819 -
obs--79.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PVSA.PARAMPVSA.TOP

+
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