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- PDB-4x5o: Human histidine tRNA synthetase -

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Basic information

Entry
Database: PDB / ID: 4x5o
TitleHuman histidine tRNA synthetase
ComponentsHistidine--tRNA ligase, cytoplasmic
KeywordsLIGASE / histidine / tRNA / synthetase
Function / homology
Function and homology information


histidine-tRNA ligase / histidine-tRNA ligase activity / histidyl-tRNA aminoacylation / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / mitochondrial translation / translation / protein homodimerization activity / mitochondrion / RNA binding ...histidine-tRNA ligase / histidine-tRNA ligase activity / histidyl-tRNA aminoacylation / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / mitochondrial translation / translation / protein homodimerization activity / mitochondrion / RNA binding / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Histidyl-anticodon-binding / Histidine-tRNA ligase / Histidine-tRNA ligase/ATP phosphoribosyltransferase regulatory subunit / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase / WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS ...Histidyl-anticodon-binding / Histidine-tRNA ligase / Histidine-tRNA ligase/ATP phosphoribosyltransferase regulatory subunit / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase / WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / Anticodon-binding domain / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / 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) / S15/NS1, RNA-binding / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Histidine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKim, Y.K. / Jeon, Y.H.
CitationJournal: Biodesign / Year: 2015
Title: Structural characteristics of human histidyl-tRNA synthetase
Authors: Kim, Y.K. / Chang, J.E. / Kim, S. / Jeon, Y.H.
History
DepositionDec 5, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histidine--tRNA ligase, cytoplasmic
B: Histidine--tRNA ligase, cytoplasmic


Theoretical massNumber of molelcules
Total (without water)114,9792
Polymers114,9792
Non-polymers00
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7780 Å2
ΔGint-44 kcal/mol
Surface area35190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.669, 97.669, 254.409
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Histidine--tRNA ligase, cytoplasmic / Histidyl-tRNA synthetase / HisRS


Mass: 57489.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HARS, HRS / Production host: Escherichia coli (E. coli) / References: UniProt: P12081, histidine-tRNA ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.38 % / Description: stick-shaped
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.29 mM potassium sodium tartrate tetrahydrate, 18 % polyethylene glycol 3350
PH range: 7-7.5

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 31689 / % possible obs: 97 % / Redundancy: 12.3 % / Net I/σ(I): 16.4

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data processing
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KMM

1kmm


Resolution: 2.8→29.021 Å / SU ML: 0.44 / Cross valid method: NONE / σ(F): 1.46 / Phase error: 32.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3136 1981 6.52 %
Rwork0.2476 --
obs0.2518 30399 97.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→29.021 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6245 0 0 11 6256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046332
X-RAY DIFFRACTIONf_angle_d0.9058513
X-RAY DIFFRACTIONf_dihedral_angle_d16.0072439
X-RAY DIFFRACTIONf_chiral_restr0.031970
X-RAY DIFFRACTIONf_plane_restr0.0031087
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.870.37711270.29871827X-RAY DIFFRACTION89
2.87-2.94760.39081340.30181913X-RAY DIFFRACTION95
2.9476-3.03420.41181370.30281976X-RAY DIFFRACTION97
3.0342-3.1320.35121390.29452006X-RAY DIFFRACTION98
3.132-3.24380.36341410.27932002X-RAY DIFFRACTION98
3.2438-3.37350.38421410.27422024X-RAY DIFFRACTION98
3.3735-3.52680.3351400.25242021X-RAY DIFFRACTION98
3.5268-3.71240.31851420.25332030X-RAY DIFFRACTION99
3.7124-3.94450.29621430.23322050X-RAY DIFFRACTION99
3.9445-4.24810.31261440.22742068X-RAY DIFFRACTION99
4.2481-4.67410.3031440.20582070X-RAY DIFFRACTION99
4.6741-5.34670.29251470.21272093X-RAY DIFFRACTION99
5.3467-6.72250.31311480.262123X-RAY DIFFRACTION99
6.7225-29.02240.26731540.24882215X-RAY DIFFRACTION97

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