[English] 日本語
Yorodumi
- PDB-6oiu: X-ray crystal structure of the ectodomain of the Toxoplasma gondi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6oiu
TitleX-ray crystal structure of the ectodomain of the Toxoplasma gondii ME49 Aminopeptidase N (TGME49_224350)
ComponentsAminopeptidase N
KeywordsHYDROLASE / Aminopeptidase N / M1 aminopeptidase / metallo-exopeptidase
Function / homology
Function and homology information


membrane alanyl aminopeptidase / aminopeptidase activity / metallopeptidase activity / membrane => GO:0016020 / zinc ion binding
Similarity search - Function
Peptidase M1, alanyl aminopeptidase / Peptidase M1, alanyl aminopeptidase, C-terminal / Peptidase M1, alanyl aminopeptidase, Ig-like fold / Peptidase M1, alanyl aminopeptidase, C-terminal domain superfamily / Alanyl aminopeptidase, Ig-like domain superfamily / Domain of unknown function (DUF3458) Ig-like fold / Domain of unknown function (DUF3458_C) ARM repeats / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Peptidase family M1 domain ...Peptidase M1, alanyl aminopeptidase / Peptidase M1, alanyl aminopeptidase, C-terminal / Peptidase M1, alanyl aminopeptidase, Ig-like fold / Peptidase M1, alanyl aminopeptidase, C-terminal domain superfamily / Alanyl aminopeptidase, Ig-like domain superfamily / Domain of unknown function (DUF3458) Ig-like fold / Domain of unknown function (DUF3458_C) ARM repeats / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy / Peptidase M4/M1, CTD superfamily
Similarity search - Domain/homology
Aminopeptidase N, putative
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMcGowan, S. / Drinkwater, N.
CitationJournal: Biochem.J. / Year: 2020
Title: X-ray crystal structure and specificity of the Toxoplasma gondii ME49 TgAPN2.
Authors: Marijanovic, E.M. / Weronika Swiderska, K. / Andersen, J. / Aschenbrenner, J.C. / Webb, C.T. / Drag, M. / Drinkwater, N. / McGowan, S.
History
DepositionApr 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aminopeptidase N
B: Aminopeptidase N
C: Aminopeptidase N
D: Aminopeptidase N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)413,54821
Polymers412,1964
Non-polymers1,35217
Water49,4692746
1
A: Aminopeptidase N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,4566
Polymers103,0491
Non-polymers4075
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Aminopeptidase N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,4566
Polymers103,0491
Non-polymers4075
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Aminopeptidase N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,4566
Polymers103,0491
Non-polymers4075
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Aminopeptidase N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,1803
Polymers103,0491
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.930, 207.874, 102.867
Angle α, β, γ (deg.)90.00, 94.34, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein
Aminopeptidase N


Mass: 103048.969 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (strain ATCC 50611 / Me49) (eukaryote)
Strain: ATCC 50611 / Me49 / Gene: TGME49_224350 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: S8G5K8, membrane alanyl aminopeptidase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2746 / 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: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 28 % PEG 3350, 0.1M Bis-Tris pH 5.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9536 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 2.2→38.54 Å / Num. obs: 195835 / % possible obs: 99.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 23.92 Å2 / Net I/σ(I): 5.3
Reflection shellResolution: 2.2→2.24 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 19286 / % possible all: 96

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EBG

3ebg


Resolution: 2.2→38.54 Å / SU ML: 0.292 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.335
RfactorNum. reflection% reflection
Rfree0.236 9637 4.92 %
Rwork0.19 --
obs0.193 195691 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 29.26 Å2
Refinement stepCycle: LAST / Resolution: 2.2→38.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27589 0 62 2746 30397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00128194
X-RAY DIFFRACTIONf_angle_d0.39938224
X-RAY DIFFRACTIONf_dihedral_angle_d4.48816979
X-RAY DIFFRACTIONf_chiral_restr0.0364300
X-RAY DIFFRACTIONf_plane_restr0.0034999
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.31463070.26575943X-RAY DIFFRACTION96
2.23-2.250.32163360.26586205X-RAY DIFFRACTION99
2.25-2.280.31143480.26126123X-RAY DIFFRACTION99
2.28-2.310.32353050.25436174X-RAY DIFFRACTION99
2.31-2.340.29783280.25276185X-RAY DIFFRACTION99
2.34-2.370.33013060.25366179X-RAY DIFFRACTION100
2.37-2.40.32273070.24296178X-RAY DIFFRACTION100
2.4-2.440.31423310.24686205X-RAY DIFFRACTION100
2.44-2.480.32123000.24726216X-RAY DIFFRACTION100
2.48-2.520.28713090.22686226X-RAY DIFFRACTION100
2.52-2.560.27673160.21926177X-RAY DIFFRACTION100
2.56-2.610.27472880.21866219X-RAY DIFFRACTION100
2.61-2.660.26623270.21966217X-RAY DIFFRACTION100
2.66-2.710.29122800.22066244X-RAY DIFFRACTION100
2.71-2.770.28713110.20716190X-RAY DIFFRACTION100
2.77-2.840.25113140.20336195X-RAY DIFFRACTION100
2.84-2.910.27013170.20066226X-RAY DIFFRACTION100
2.91-2.990.26063090.20556189X-RAY DIFFRACTION100
2.99-3.070.23883150.19676255X-RAY DIFFRACTION100
3.07-3.170.23253320.1886197X-RAY DIFFRACTION100
3.17-3.290.23063380.18256230X-RAY DIFFRACTION100
3.29-3.420.20853180.18176228X-RAY DIFFRACTION100
3.42-3.570.22393590.17266186X-RAY DIFFRACTION100
3.57-3.760.2122970.16166214X-RAY DIFFRACTION100
3.76-40.1873060.15766276X-RAY DIFFRACTION100
4-4.30.20263280.15346240X-RAY DIFFRACTION100
4.3-4.740.18763300.13856216X-RAY DIFFRACTION100
4.74-5.420.17173530.14876227X-RAY DIFFRACTION100
5.42-6.820.19673570.17666228X-RAY DIFFRACTION100
6.82-38.550.17793650.15756266X-RAY DIFFRACTION100

+
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://pdbjlc1.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