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- PDB-6o76: Human cytosolic Histidyl-tRNA synthetase (HisRS) with WHEP domain -

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Basic information

Entry
Database: PDB / ID: 6o76
TitleHuman cytosolic Histidyl-tRNA synthetase (HisRS) with WHEP domain
ComponentsHistidine--tRNA ligase, cytoplasmic
KeywordsLIGASE / tRNA / CMT / WHEP domain / alpha beta domain
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: 2.787 Å
AuthorsKuhle, B. / Yang, X.L.
Citation
Journal: Biodesign / Year: 2014
Title: Structural characteristics of human histidyl-tRNA synthetase
Authors: Kim, Y.K. / Chang, J.E. / Kim, S. / Jeon, Y.H.
#1: Journal: J. Biol. Chem. / Year: 2019
Title: Neurodegenerative Charcot-Marie-Tooth disease as a case study to decipher novel functions of aminoacyl-tRNA synthetases.
Authors: Wei, N. / Zhang, Q. / Yang, X.L.
History
DepositionMar 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)115,0504
Polymers114,9792
Non-polymers712
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8200 Å2
ΔGint-57 kcal/mol
Surface area40030 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 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P12081, histidine-tRNA ligase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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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: 2.64 Å3/Da / Density % sol: 53.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.29 mM potassium sodium tartrate tetrahydrate, 18% PEG3350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 18, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.787→30 Å / Num. obs: 31689 / % possible obs: 97 % / Redundancy: 12.3 % / Biso Wilson estimate: 65.07 Å2 / Net I/σ(I): 16.4
Reflection shellResolution: 2.787→2.87 Å / Num. unique obs: 1954

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4X5O

4x5o


Resolution: 2.787→29.021 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 30.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2952 1555 5.07 %
Rwork0.2358 --
obs0.2388 30685 96.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.787→29.021 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6940 0 2 62 7004
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087176
X-RAY DIFFRACTIONf_angle_d1.4249658
X-RAY DIFFRACTIONf_dihedral_angle_d17.5064409
X-RAY DIFFRACTIONf_chiral_restr0.0751111
X-RAY DIFFRACTIONf_plane_restr0.0071235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7865-2.87640.38291090.34872300X-RAY DIFFRACTION85
2.8764-2.97910.38391370.3232532X-RAY DIFFRACTION95
2.9791-3.09820.34411210.29622619X-RAY DIFFRACTION97
3.0982-3.23910.3441370.28422649X-RAY DIFFRACTION98
3.2391-3.40960.32071450.26132638X-RAY DIFFRACTION98
3.4096-3.62280.29361590.24372650X-RAY DIFFRACTION98
3.6228-3.90190.26631510.22172677X-RAY DIFFRACTION99
3.9019-4.29350.2581480.20762689X-RAY DIFFRACTION99
4.2935-4.91220.2321410.1822737X-RAY DIFFRACTION99
4.9122-6.1790.29371650.23272750X-RAY DIFFRACTION99
6.179-29.02240.31461420.22712889X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.05120.8979-1.30411.9516-1.18934.9120.1519-0.35570.16880.2105-0.1217-0.1622-0.31150.6323-0.02490.36440.1230.03040.5394-0.10580.4233130.0159-36.1987264.5685
26.2812-1.5581-1.25221.33880.16891.1985-0.2988-0.3713-0.21770.08450.1899-0.36640.15840.53670.0870.60950.09430.0980.6641-0.05180.4665143.1485-56.8509277.8648
34.6167-1.2891-0.47923.4994-3.04924.33690.0416-0.262-0.3586-0.1972-0.06920.05170.30720.7409-0.03220.30730.0786-0.02010.5279-0.08880.5187131.8254-45.5199267.5682
44.63141.7724-0.57755.97840.46697.52870.14230.3371-0.0924-0.6053-0.16920.66410.2052-0.41940.05020.64890.1163-0.1720.3995-0.18950.4992101.4203-39.9484234.6204
52.48170.74490.73478.2613-0.79260.36550.68350.3475-0.6404-0.86-0.7403-1.41331.87580.3452-0.29971.68980.53880.01081.74350.43721.1788107.8708-8.5363269.5961
64.04860.89920.32413.14781.26755.2436-0.0138-0.20680.3918-0.39920.0509-0.185-0.87510.2350.02450.5229-0.00530.08060.3143-0.09110.4325121.9456-24.0255251.7036
71.1262-0.58951.05281.59111.60754.6365-1.37650.17581.9759-1.45560.19630.5172-4.07091.30840.43093.5163-0.0376-1.38280.80310.03761.8758112.75691.8726241.3898
81.510.16510.47470.46530.63140.8866-1.00080.56951.6914-2.133-0.06690.8995-1.93540.4040.51132.43470.3326-1.14320.94490.03681.4557102.8019-8.7536232.0506
92.5655-1.41042.23313.62720.12385.0177-0.60970.07620.958-0.9784-0.38180.1116-2.0512-0.05020.55841.31160.0402-0.2850.4340.00780.7978113.2479-16.4788247.2719
104.5722-0.7186-0.99684.0762-0.54525.11570.1028-0.299-0.23240.069-0.02640.30190.3244-0.5415-0.10960.3523-0.03330.08580.6914-0.08830.4021106.3569-48.6474281.6785
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 54 through 206 )
2X-RAY DIFFRACTION2chain 'A' and (resid 207 through 333 )
3X-RAY DIFFRACTION3chain 'A' and (resid 334 through 400 )
4X-RAY DIFFRACTION4chain 'A' and (resid 401 through 503 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 44 )
6X-RAY DIFFRACTION6chain 'B' and (resid 45 through 209 )
7X-RAY DIFFRACTION7chain 'B' and (resid 210 through 271 )
8X-RAY DIFFRACTION8chain 'B' and (resid 272 through 312 )
9X-RAY DIFFRACTION9chain 'B' and (resid 313 through 400 )
10X-RAY DIFFRACTION10chain 'B' and (resid 401 through 502 )

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