[English] 日本語
Yorodumi
- PDB-7wfx: EVAA-KlAte1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7wfx
TitleEVAA-KlAte1
ComponentsArginyltransferase
KeywordsTRANSFERASE / Arginyl-tRNA protein transferase 1
Function / homology
Function and homology information


arginyltransferase / arginyl-tRNA--protein transferase activity / metal ion binding / cytoplasm
Similarity search - Function
N-end aminoacyl transferase, N-terminal / N-end rule aminoacyl transferase, C-terminal / N-end rule aminoacyl transferase / Arginine-tRNA-protein transferase, N terminus / Arginine-tRNA-protein transferase, C terminus / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsKim, M.K. / Kim, B.H. / Oh, S.-J. / Song, H.K.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Crystal structure of the Ate1 arginyl-tRNA-protein transferase and arginylation of N-degron substrates.
Authors: Kim, B.H. / Kim, M.K. / Oh, S.J. / Nguyen, K.T. / Kim, J.H. / Varshavsky, A. / Hwang, C.S. / Song, H.K.
History
DepositionDec 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Arginyltransferase
B: Arginyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,0154
Polymers115,8852
Non-polymers1312
Water13,727762
1
A: Arginyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0082
Polymers57,9421
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Arginyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0082
Polymers57,9421
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.720, 114.505, 159.469
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Arginyltransferase / Arginyl-tRNA protein transferase 1


Mass: 57942.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Gene: KLLA0_A04862g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CXX6, arginyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 762 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.21 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 120mM alcohols (Molecular dimensions), 100mM buffer system 2 pH 7.5 (Molecular dimensions), 37.5% (v/v) precipitant Mix 4 (Molecular dimensions)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 93872 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / CC1/2: 0.985 / CC star: 0.996 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.071 / Rrim(I) all: 0.163 / Rsym value: 0.146 / Χ2: 0.623 / Net I/σ(I): 10.848
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.444 / Num. unique obs: 4641 / CC1/2: 0.551 / CC star: 0.843 / Rpim(I) all: 0.461 / Rrim(I) all: 0.893 / Rsym value: 0.76 / Χ2: 0.46 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.95→46.51 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2016 1997 2.13 %
Rwork0.1635 --
obs0.1643 93774 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→46.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7954 0 2 762 8718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118146
X-RAY DIFFRACTIONf_angle_d1.07211031
X-RAY DIFFRACTIONf_dihedral_angle_d5.7871071
X-RAY DIFFRACTIONf_chiral_restr0.0631196
X-RAY DIFFRACTIONf_plane_restr0.011413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.990.28211350.22466280X-RAY DIFFRACTION96
1.99-2.050.21721420.20896488X-RAY DIFFRACTION100
2.05-2.110.25721410.19716496X-RAY DIFFRACTION100
2.11-2.180.21581420.17696522X-RAY DIFFRACTION100
2.18-2.250.18051420.16196515X-RAY DIFFRACTION100
2.25-2.340.20621430.16046543X-RAY DIFFRACTION100
2.34-2.450.19511420.15616538X-RAY DIFFRACTION100
2.45-2.580.20371430.15796562X-RAY DIFFRACTION100
2.58-2.740.18821420.15936550X-RAY DIFFRACTION100
2.74-2.950.20781430.16616563X-RAY DIFFRACTION100
2.95-3.250.20741440.16756605X-RAY DIFFRACTION100
3.25-3.720.20031450.15656652X-RAY DIFFRACTION100
3.72-4.690.16451450.13826647X-RAY DIFFRACTION99
4.69-46.510.21521480.16666816X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 6.2888 Å / Origin y: 119.751 Å / Origin z: 169.1095 Å
111213212223313233
T0.1091 Å20.0007 Å20.015 Å2-0.1117 Å20.0289 Å2--0.1134 Å2
L0.2295 °2-0.0295 °20.1702 °2-0.2041 °20.1348 °2--0.4072 °2
S-0.0047 Å °-0.0404 Å °-0.0017 Å °0.0497 Å °0.0054 Å °0.0239 Å °-0.0036 Å °-0.0663 Å °-0.0001 Å °
Refinement TLS groupSelection details: all

+
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