[English] 日本語
Yorodumi
- PDB-8p42: Full length structure of TcMIP with bound inhibitor NJS227. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8p42
TitleFull length structure of TcMIP with bound inhibitor NJS227.
ComponentsMacrophage infectivity potentiator
KeywordsSTRUCTURAL PROTEIN / Macrophage / potentiator / soluble / protein
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / chromatin / nucleolus / extracellular region
Similarity search - Function
FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / : / Macrophage infectivity potentiator
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsWhittaker, J.J. / Guskov, A. / Goretzki, B. / Hellmich, U.A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)390713860 Germany
CitationJournal: To Be Published
Title: Structural dynamics of macrophage infectivity potentiator proteins (MIPs) are differentially modulated by inhibitors and appendage domains
Authors: Whittaker, J.J. / Guskov, A. / Goretzki, B. / Hellmich, U.A.
History
DepositionMay 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Macrophage infectivity potentiator
D: Macrophage infectivity potentiator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9118
Polymers36,3732
Non-polymers1,5386
Water1,27971
1
A: Macrophage infectivity potentiator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0625
Polymers18,1871
Non-polymers8754
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Macrophage infectivity potentiator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8493
Polymers18,1871
Non-polymers6632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.744, 87.744, 57.505
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein Macrophage infectivity potentiator / Peptidyl-prolyl cis-trans isomerase / PPIase / Rotamase


Mass: 18186.549 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: MIP / Production host: Escherichia coli (E. coli) / References: UniProt: Q09734, peptidylprolyl isomerase
#2: Chemical ChemComp-WRX / (2~{S})-1-[(4-fluorophenyl)methylsulfonyl]-~{N}-[(2~{S})-3-(4-fluorophenyl)-1-oxidanylidene-1-(pyridin-3-ylmethylamino)propan-2-yl]piperidine-2-carboxamide


Mass: 556.624 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H30F2N4O4S
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 5mM TRIS pH 7.5 150mM NaCl PEG2000 12 %

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.967 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967 Å / Relative weight: 1
ReflectionResolution: 2.64→34.9 Å / Num. obs: 12330 / % possible obs: 94.84 % / Redundancy: 9 % / CC1/2: 0.92 / Net I/σ(I): 13.2
Reflection shellResolution: 2.64→2.74 Å / Num. unique obs: 1225 / CC1/2: 0.84

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→34.88 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2819 649 5.27 %
Rwork0.2241 --
obs0.227 12326 94.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.64→34.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2522 0 106 71 2699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032674
X-RAY DIFFRACTIONf_angle_d0.6843587
X-RAY DIFFRACTIONf_dihedral_angle_d9.207404
X-RAY DIFFRACTIONf_chiral_restr0.056361
X-RAY DIFFRACTIONf_plane_restr0.006475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.64-2.850.35541350.31332303X-RAY DIFFRACTION95
2.85-3.130.30291170.26522359X-RAY DIFFRACTION96
3.13-3.590.33071580.25562350X-RAY DIFFRACTION97
3.59-4.510.25961260.21012291X-RAY DIFFRACTION93
4.52-34.880.22431130.17222374X-RAY DIFFRACTION93

+
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