[English] 日本語
Yorodumi
- PDB-3hfv: Crystal structure of human mitochondrial phenylalanyl-tRNA synthe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hfv
TitleCrystal structure of human mitochondrial phenylalanyl-tRNA synthetase complexed with m-tyrosine
ComponentsPhenylalanyl-tRNA synthetase, mitochondrial
KeywordsLIGASE / CLASSII AARSS FOLD / RRM DOMAIN / TRNA / RNA RECOGNTION / AMINOACYL-TRNA SYNTHETASE / ATP-BINDING / MITOCHONDRION / NUCLEOTIDE-BINDING / PROTEIN BIOSYNTHESIS / TRANSIT PEPTIDE / M-TYROSINE / Polymorphism
Function / homology
Function and homology information


phenylalanine-tRNA ligase / Mitochondrial tRNA aminoacylation / phenylalanine-tRNA ligase activity / phenylalanyl-tRNA aminoacylation / tRNA aminoacylation for protein translation / tRNA processing / tRNA binding / mitochondrial matrix / mitochondrion / ATP binding / cytoplasm
Similarity search - Function
Phenylalanyl-tRNA synthetase, class IIc, mitochondrial / Ferrodoxin-fold anticodon-binding domain / Ferrodoxin-fold anticodon-binding domain / Ferrodoxin-fold anticodon-binding domain superfamily / Ferredoxin-fold anticodon binding domain / Ferredoxin-fold anticodon binding (FDX-ACB) domain profile. / Ferredoxin-fold anticodon binding domain / Phenylalanyl-tRNA synthetase / tRNA synthetases class II core domain (F) / Bira Bifunctional Protein; Domain 2 ...Phenylalanyl-tRNA synthetase, class IIc, mitochondrial / Ferrodoxin-fold anticodon-binding domain / Ferrodoxin-fold anticodon-binding domain / Ferrodoxin-fold anticodon-binding domain superfamily / Ferredoxin-fold anticodon binding domain / Ferredoxin-fold anticodon binding (FDX-ACB) domain profile. / Ferredoxin-fold anticodon binding domain / Phenylalanyl-tRNA synthetase / tRNA synthetases class II core domain (F) / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
META-TYROSINE / Phenylalanine--tRNA ligase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKlipcan, L. / Moor, N. / Kessler, N. / Safro, M.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Eukaryotic cytosolic and mitochondrial phenylalanyl-tRNA synthetases catalyze the charging of tRNA with the meta-tyrosine
Authors: Klipcan, L. / Moor, N. / Kessler, N. / Safro, M.G.
History
DepositionMay 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phenylalanyl-tRNA synthetase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6872
Polymers48,5061
Non-polymers1811
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.640, 90.143, 97.133
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Phenylalanyl-tRNA synthetase, mitochondrial / Phenylalanine--tRNA ligase / PheRS


Mass: 48506.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FARS2, FARS1, HSPC320 / Production host: Escherichia coli (E. coli) / References: UniProt: O95363, phenylalanine-tRNA ligase
#2: Chemical ChemComp-MTY / META-TYROSINE / Tyrosine


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.47 Å3/Da / Density % sol: 50.12 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.8M Ammonium acetate, 0.1M Tris-Propane, 0.1M Magnesium chloride, 0,05M DTT, VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 5, 2008
RadiationMonochromator: Aluminium or Carbon foils / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.6→28.7 Å / Num. all: 14700 / Num. obs: 14667 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.597→2.665 Å / % possible all: 93.19

-
Processing

Software
NameVersionClassification
REFMAC5.4.0067refinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1CMQ

1cmq


Resolution: 2.6→28.7 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.918 / SU B: 11.662 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.256 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23939 731 5 %RANDOM
Rwork0.192 ---
all0.1944 13969 --
obs0.1944 13969 95.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.119 Å2
Baniso -1Baniso -2Baniso -3
1-1.95 Å20 Å20 Å2
2---1.22 Å20 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 2.6→28.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3354 0 13 83 3450
Refine LS restraintsType: r_dihedral_angle_1_deg / Dev ideal: 1.57
LS refinement shellResolution: 2.597→2.665 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 42 -
Rwork0.325 984 -
obs--93.19 %

+
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