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- PDB-4g85: Crystal structure of human HisRS -

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Basic information

Entry
Database: PDB / ID: 4g85
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 / 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: 3.11 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)116,8592
Polymers116,8592
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7560 Å2
ΔGint-46 kcal/mol
Surface area36860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.449, 100.449, 257.131
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A1 - 9999
2115B1 - 9999

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Components

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


Mass: 58429.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HARS, HRS / Plasmid: PET32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12081, histidine-tRNA ligase

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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: 2.78 Å3/Da / Density % sol: 55.68 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M ammonium citrate 20% PEGMME 2000, pH 7.5, 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: 3.1→50 Å / Num. obs: 24210 / % possible obs: 98.8 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.069 / Χ2: 1.012 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.1-3.155.60.69611910.821199.9
3.15-3.215.60.55212030.824199.8
3.21-3.275.60.49111680.827199.9
3.27-3.345.70.41212020.897199.8
3.34-3.415.60.32211970.938199.9
3.41-3.495.60.27112011.016199.8
3.49-3.585.60.23312101.014199.8
3.58-3.685.60.20611911.059199.8
3.68-3.785.60.16412031.102199.8
3.78-3.915.60.12911991.194199.6
3.91-4.045.60.10612111.172199.6
4.04-4.215.50.09311971.169199.2
4.21-4.45.40.08312001.158199.1
4.4-4.635.40.0712091.119198.9
4.63-4.925.40.06612221.024198.9
4.92-5.35.40.06712311.136199.2
5.3-5.835.40.0612340.964199.2
5.83-6.675.40.04512560.893199.1
6.67-8.45.30.03112610.903198.4
8.4-504.80.02512241.031187.2

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0072refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HRI

3hri


Resolution: 3.11→50 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.859 / Occupancy max: 1 / Occupancy min: 1 / SU B: 64.217 / SU ML: 0.502 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.557 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3273 1213 5.1 %RANDOM
Rwork0.2711 ---
obs0.2738 23872 97.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 73.02 Å2 / Biso mean: 107.392 Å2 / Biso min: 46.26 Å2
Baniso -1Baniso -2Baniso -3
1-3.46 Å2-0 Å2-0 Å2
2--3.46 Å20 Å2
3----6.92 Å2
Refinement stepCycle: LAST / Resolution: 3.11→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6432 0 0 0 6432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226518
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.9868823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2415841
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.50824.207271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.786151090
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0251543
X-RAY DIFFRACTIONr_chiral_restr0.1040.21040
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214848
X-RAY DIFFRACTIONr_mcbond_it0.3251.54212
X-RAY DIFFRACTIONr_mcangle_it0.66926686
X-RAY DIFFRACTIONr_scbond_it1.15532306
X-RAY DIFFRACTIONr_scangle_it2.0534.52137
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1695MEDIUM POSITIONAL0.270.5
1461LOOSE POSITIONAL0.395
1695MEDIUM THERMAL0.362
1461LOOSE THERMAL0.5410
LS refinement shellResolution: 3.11→3.188 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 76 -
Rwork0.344 1540 -
all-1616 -
obs--91.14 %
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)
11.2965-1.1121-0.38352.80861.05641.336-0.2249-0.0114-0.0220.19790.04880.24180.0998-0.31870.17610.3755-0.0178-0.11030.2970.11830.1864-34.55751.21316.239
23.0360.78180.40735.5283-2.13828.6907-0.32010.3358-0.2564-0.1502-0.0326-0.9907-0.1431.27650.35270.336-0.12720.00260.40950.20160.4234-1.47139.153-19.226
32.8122-0.9158-0.93512.29210.66344.686-0.15890.0931-1.0364-0.0226-0.02630.09781.5945-0.20050.18520.9388-0.0979-0.05250.17710.13010.5736-18.4718.039-4.825
48.6847-2.26531.79445.6494-1.7669.2209-0.2606-0.47290.81060.40670.1202-0.6231-0.48891.07060.14040.3918-0.016-0.20960.32550.01810.2442-6.15453.21628.596
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A51 - 408
2X-RAY DIFFRACTION2A409 - 503
3X-RAY DIFFRACTION3B54 - 408
4X-RAY DIFFRACTION4B409 - 503

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