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- PDB-4g84: Crystal structure of human HisRS -

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Basic information

Entry
Database: PDB / ID: 4g84
TitleCrystal structure of human HisRS
ComponentsHistidine--tRNA ligase, cytoplasmic
KeywordsLIGASE / 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 / cytosol / cytoplasm
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
IMIDAZOLE / Histidine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWei, Z. / Wu, J. / Zhou, J.J. / Yang, X.-L. / Zhang, M. / Schimmel, P.
CitationJournal: Structure / Year: 2012
Title: Internally Deleted Human tRNA Synthetase Suggests Evolutionary Pressure for Repurposing.
Authors: Xu, Z. / Wei, Z. / Zhou, J.J. / Ye, F. / Lo, W.S. / Wang, F. / Lau, C.F. / Wu, J. / Nangle, L.A. / Chiang, K.P. / Yang, X.L. / Zhang, M. / Schimmel, P.
History
DepositionJul 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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

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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)105,2566
Polymers105,0132
Non-polymers2434
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8230 Å2
ΔGint-38 kcal/mol
Surface area36490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.519, 93.519, 254.533
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 52506.434 Da / Num. of mol.: 2 / Fragment: UNP residues 54-506
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HARS, HRS / Plasmid: PET32m / Production host: Escherichia coli (E. coli) / References: UniProt: P12081, histidine-tRNA ligase
#2: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.65 Å3/Da / Density % sol: 53.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M imidazole 20% v/v PEGMME550, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 45571 / % possible obs: 99.8 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.074 / Χ2: 0.959 / Net I/σ(I): 10.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.445.80.67922120.878199.9
2.44-2.495.80.55322330.889199.9
2.49-2.535.90.49122520.8751100
2.53-2.595.90.40322320.8891100
2.59-2.6460.36622240.8811100
2.64-2.76.10.32322480.8961100
2.7-2.776.20.2722730.9191100
2.77-2.856.30.21422410.9211100
2.85-2.936.40.17122340.9571100
2.93-3.026.40.14722670.9931100
3.02-3.136.50.11822630.9811100
3.13-3.266.50.09322511.0211100
3.26-3.416.50.0822700.9861100
3.41-3.586.40.06822791.0531100
3.58-3.816.40.06222731.0221100
3.81-4.16.30.05523001.0021100
4.1-4.526.10.05723041.046199.8
4.52-5.175.90.05523311.009199.7
5.17-6.5160.04923680.954199.8
6.51-505.40.03225160.964198.2

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
PHASERphasing
PHENIX1.6.4_486refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G85

4g85


Resolution: 2.4→32.002 Å / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.35 / σ(F): 0 / Phase error: 25.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2498 2124 5.05 %
Rwork0.191 --
obs0.194 42096 93.27 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.315 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso max: 207.79 Å2 / Biso mean: 54.3744 Å2 / Biso min: 17.32 Å2
Baniso -1Baniso -2Baniso -3
1-5.3455 Å20 Å2-0 Å2
2--5.3455 Å2-0 Å2
3----10.6909 Å2
Refinement stepCycle: LAST / Resolution: 2.4→32.002 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6903 0 16 166 7085
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)
10.53880.2210.66890.74161.09372.0536-0.024-0.08890.01080.0421-0.105-0.035-0.1622-0.28980.09560.18320.04720.03660.14570.00120.1216-28.893636.354611.8789
21.2747-0.74510.00180.44470.49290.41940.11370.03160.1444-0.1581-0.23650.1692-0.4359-0.03160.12430.34840.146-0.13830.1807-0.08740.2734-40.939258.214623.8484
30.4470.2316-0.31781.30170.79250.9304-0.16860.06430.0138-0.2859-0.14380.113-0.0363-0.2750.23130.31950.0384-0.04630.1612-0.02790.2058-30.282245.46612.7382
40.93760.9104-0.34281.32-0.79510.6212-0.0120.0094-0.08910.0208-0.0059-0.1039-0.20140.06860.00990.2254-0.07330.03340.17370.0130.1671-2.198833.6399-20.9169
50.3387-0.5697-0.56790.45940.34641.919-0.02790.0481-0.02610.037-0.08160.02670.2679-0.23590.11760.264-0.10540.01530.08750.00080.1153-27.971322.66624.2701
61.24790.82160.47040.10710.74941.38840.19650.0359-0.41980.28190.0278-0.40890.4388-0.0944-0.22460.3779-0.0209-0.11790.1066-0.00350.3329-14.32163.6453-13.3401
71.9388-0.29641.23680.15570.62582.70020.1711-0.1385-0.4370.15120.05780.04860.7675-0.1423-0.20870.4052-0.0728-0.01470.18190.04960.2609-16.940217.0704-2.0386
81.2119-0.30280.70660.4941-0.38020.5203-0.07490.01090.11810.03680.0122-0.0455-0.04240.19720.07120.24560.0332-0.01740.19390.03140.1638-4.423248.302926.146
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 55:209 )A55 - 209
2X-RAY DIFFRACTION2( CHAIN A AND RESID 210:326 )A210 - 326
3X-RAY DIFFRACTION3( CHAIN A AND RESID 327:404 )A327 - 404
4X-RAY DIFFRACTION4( CHAIN A AND RESID 405:504 )A405 - 504
5X-RAY DIFFRACTION5( CHAIN B AND RESID 43:172 )B43 - 172
6X-RAY DIFFRACTION6( CHAIN B AND RESID 173:336 )B173 - 336
7X-RAY DIFFRACTION7( CHAIN B AND RESID 337:404 )B337 - 404
8X-RAY DIFFRACTION8( CHAIN B AND RESID 405:504 )B405 - 504

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