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- PDB-3l4g: Crystal structure of Homo Sapiens cytoplasmic Phenylalanyl-tRNA s... -

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Basic information

Entry
Database: PDB / ID: 3l4g
TitleCrystal structure of Homo Sapiens cytoplasmic Phenylalanyl-tRNA synthetase
Components
  • Phenylalanyl-tRNA synthetase alpha chain
  • Phenylalanyl-tRNA synthetase beta chain
KeywordsLIGASE / aminoacylation / tRNA-binding / DNA-binding domain / four-helix bundle / Acetylation / Aminoacyl-tRNA synthetase / ATP-binding / Cytoplasm / Nucleotide-binding / Phosphoprotein / Polymorphism / Protein biosynthesis
Function / homology
Function and homology information


phenylalanine-tRNA ligase complex / phenylalanine-tRNA ligase / phenylalanyl-tRNA aminoacylation / phenylalanine-tRNA ligase activity / Cytosolic tRNA aminoacylation / protein heterotetramerization / tRNA binding / translation / magnesium ion binding / RNA binding ...phenylalanine-tRNA ligase complex / phenylalanine-tRNA ligase / phenylalanyl-tRNA aminoacylation / phenylalanine-tRNA ligase activity / Cytosolic tRNA aminoacylation / protein heterotetramerization / tRNA binding / translation / magnesium ion binding / RNA binding / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
Arc Repressor Mutant, subunit A - #2320 / Arc Repressor Mutant, subunit A - #2330 / Ribosomal Protein S8; Chain: A, domain 1 - #240 / PheRS DNA binding domain 2 / PheRS, DNA binding domain 1 / PheRS, DNA binding domain 3 / PheRS DNA binding domain 1 / PheRS DNA binding domain 3 / PheRS DNA binding domain 2 / Phenylalanine--tRNA ligase beta subunit, B1 domain ...Arc Repressor Mutant, subunit A - #2320 / Arc Repressor Mutant, subunit A - #2330 / Ribosomal Protein S8; Chain: A, domain 1 - #240 / PheRS DNA binding domain 2 / PheRS, DNA binding domain 1 / PheRS, DNA binding domain 3 / PheRS DNA binding domain 1 / PheRS DNA binding domain 3 / PheRS DNA binding domain 2 / Phenylalanine--tRNA ligase beta subunit, B1 domain / Phe-tRNA synthetase beta subunit B1 domain / Phenylalanyl-tRNA synthetase, class IIc, beta subunit, archaeal/eukaryotic type / Phenylalanyl-tRNA Synthetase; Chain B, domain 3 / Phenylalanyl-trna Synthetase, Chain B, domain 3 / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 - #10 / Phenylalanyl-tRNA synthetase, class IIc, alpha subunit / tRNA synthetase, B5-domain / tRNA synthetase B5 domain / B5 domain profile. / tRNA synthetase B5 domain / B3/4 domain / Phenylalanyl tRNA synthetase beta chain, core domain / Phenylalanyl tRNA synthetase beta chain CLM domain / Phenylalanine-tRNA ligase, class IIc, beta subunit / B3/B4 tRNA-binding domain / Phenylalanyl-tRNA synthetase-like, B3/B4 / B3/4 domain / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 / Phenylalanyl-tRNA synthetase / tRNA synthetases class II core domain (F) / Putative DNA-binding domain superfamily / Ribosomal Protein S8; Chain: A, domain 1 / 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) / 3-Layer(bba) Sandwich / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHENYLALANINE / Phenylalanine--tRNA ligase beta subunit / Phenylalanine--tRNA ligase alpha subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsFinarov, I. / Moor, N. / Kessler, N. / Klipcan, L. / Safro, M.G.
Citation
Journal: Structure / Year: 2010
Title: Structure of human cytosolic phenylalanyl-tRNA synthetase: evidence for kingdom-specific design of the active sites and tRNA binding patterns.
Authors: Finarov, I. / Moor, N. / Kessler, N. / Klipcan, L. / Safro, M.G.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Crystallization and X-ray analysis of human cytoplasmic phenylalanyl-tRNA synthetase
Authors: Finarov, I. / Moor, N. / Kessler, N. / Safro, M.G.
History
DepositionDec 20, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phenylalanyl-tRNA synthetase alpha chain
B: Phenylalanyl-tRNA synthetase beta chain
C: Phenylalanyl-tRNA synthetase alpha chain
D: Phenylalanyl-tRNA synthetase beta chain
E: Phenylalanyl-tRNA synthetase alpha chain
F: Phenylalanyl-tRNA synthetase beta chain
G: Phenylalanyl-tRNA synthetase alpha chain
H: Phenylalanyl-tRNA synthetase beta chain
I: Phenylalanyl-tRNA synthetase alpha chain
J: Phenylalanyl-tRNA synthetase beta chain
K: Phenylalanyl-tRNA synthetase alpha chain
L: Phenylalanyl-tRNA synthetase beta chain
M: Phenylalanyl-tRNA synthetase alpha chain
N: Phenylalanyl-tRNA synthetase beta chain
O: Phenylalanyl-tRNA synthetase alpha chain
P: Phenylalanyl-tRNA synthetase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)992,19424
Polymers990,87216
Non-polymers1,3228
Water00
1
A: Phenylalanyl-tRNA synthetase alpha chain
B: Phenylalanyl-tRNA synthetase beta chain
C: Phenylalanyl-tRNA synthetase alpha chain
D: Phenylalanyl-tRNA synthetase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,0486
Polymers247,7184
Non-polymers3302
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25350 Å2
ΔGint-128 kcal/mol
Surface area82080 Å2
MethodPISA
2
E: Phenylalanyl-tRNA synthetase alpha chain
F: Phenylalanyl-tRNA synthetase beta chain
G: Phenylalanyl-tRNA synthetase alpha chain
H: Phenylalanyl-tRNA synthetase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,0486
Polymers247,7184
Non-polymers3302
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24950 Å2
ΔGint-121 kcal/mol
Surface area70230 Å2
MethodPISA
3
I: Phenylalanyl-tRNA synthetase alpha chain
J: Phenylalanyl-tRNA synthetase beta chain
K: Phenylalanyl-tRNA synthetase alpha chain
L: Phenylalanyl-tRNA synthetase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,0486
Polymers247,7184
Non-polymers3302
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24650 Å2
ΔGint-123 kcal/mol
Surface area73250 Å2
MethodPISA
4
M: Phenylalanyl-tRNA synthetase alpha chain
N: Phenylalanyl-tRNA synthetase beta chain
O: Phenylalanyl-tRNA synthetase alpha chain
P: Phenylalanyl-tRNA synthetase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,0486
Polymers247,7184
Non-polymers3302
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24370 Å2
ΔGint-120 kcal/mol
Surface area71870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)363.338, 213.884, 212.957
Angle α, β, γ (deg.)90.00, 125.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Phenylalanyl-tRNA synthetase alpha chain / cytoplasmic Phenylalanyl-tRNA synthetase alpha subunit / Phenylalanine--tRNA ligase alpha chain / ...cytoplasmic Phenylalanyl-tRNA synthetase alpha subunit / Phenylalanine--tRNA ligase alpha chain / PheRS / CML33


Mass: 57644.527 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FARSA, FARS, FARSL, FARSLA / Plasmid: Pet21 / Production host: Escherichia coli (E. coli) / Strain (production host): BLR / References: UniProt: Q9Y285, phenylalanine-tRNA ligase
#2: Protein
Phenylalanyl-tRNA synthetase beta chain / cytoplasmic Phenylalanyl-tRNA synthetase beta subunit / Phenylalanine--tRNA ligase beta chain / PheRS


Mass: 66214.484 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FARSB, FARSLB, FRSB, HSPC173 / Plasmid: PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BLR / References: UniProt: Q9NSD9, phenylalanine-tRNA ligase
#3: Chemical
ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C9H11NO2

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.41 Å3/Da / Density % sol: 63.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 1.04M NaCitrate, MES pH 6.4, 5mM 2-mercaptoethanol, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 14, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. all: 199279 / Num. obs: 193345 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rmerge(I) obs: 0.071
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.658 / Mean I/σ(I) obs: 1.24 / % possible all: 96.8

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PYS and 2CXI

1pys

2cxi


Resolution: 3.3→30 Å / Cross valid method: THROUGHOUT / σ(F): 1778 / Stereochemistry target values: Engh & Huber
Details: a non-crystallographic symmetry for most parts of the molecules in assymetric unit was used
RfactorNum. reflection% reflectionSelection details
Rfree0.287 9560 -Random
Rwork0.242 ---
obs0.242 191242 96 %-
all-199279 --
Solvent computationBsol: 105.879 Å2
Displacement parametersBiso mean: 120.6 Å2
Baniso -1Baniso -2Baniso -3
1--10.507 Å20 Å210.166 Å2
2--17.115 Å20 Å2
3----6.608 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.49 Å
Luzzati d res low-5 Å
Luzzati sigma a0.87 Å0.85 Å
Refinement stepCycle: LAST / Resolution: 3.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms59299 0 96 0 59395
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008687
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.42
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.34
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-ID% reflection obs (%)
3.3-3.420.39549320.3795X-RAY DIFFRACTION89.02
3.42-3.550.39138990.3562X-RAY DIFFRACTION90.39
3.55-3.720.35999600.3247X-RAY DIFFRACTION91.18
3.72-3.910.33679220.2984X-RAY DIFFRACTION91.52
3.91-4.160.30310050.2593X-RAY DIFFRACTION91.57
4.16-4.480.27159740.2219X-RAY DIFFRACTION91.75
4.48-4.930.27479650.2152X-RAY DIFFRACTION91.96
4.93-5.640.28429710.2198X-RAY DIFFRACTION91.93
5.64-7.110.28099290.2278X-RAY DIFFRACTION92.16
7.11-300.224410030.1904X-RAY DIFFRACTION90.07

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