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- PDB-4xeo: Crystal Structure of human AlaRS catalytic domain with R329H mutation -

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Basic information

Entry
Database: PDB / ID: 4xeo
TitleCrystal Structure of human AlaRS catalytic domain with R329H mutation
ComponentsAlanine--tRNA ligase, cytoplasmic
KeywordsLIGASE / tRNA synthetase / CMT
Function / homology
Function and homology information


regulation of cytoplasmic translational fidelity / Ser-tRNA(Ala) hydrolase activity / Ligases / alanine-tRNA ligase / alanine-tRNA ligase activity / alanyl-tRNA aminoacylation / cerebellar Purkinje cell layer development / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / aminoacyl-tRNA editing activity ...regulation of cytoplasmic translational fidelity / Ser-tRNA(Ala) hydrolase activity / Ligases / alanine-tRNA ligase / alanine-tRNA ligase activity / alanyl-tRNA aminoacylation / cerebellar Purkinje cell layer development / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / aminoacyl-tRNA editing activity / tRNA modification / tRNA processing / amino acid binding / neuromuscular process controlling balance / neuron apoptotic process / negative regulation of neuron apoptotic process / tRNA binding / mitochondrion / extracellular exosome / zinc ion binding / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
Alanine-tRNA ligase, eukaryota/bacteria / Alanine-tRNA ligase, class IIc / Alanine-tRNA ligase, class IIc, anti-codon-binding domain superfamily / : / Alanyl-tRNA synthetase, class IIc, N-terminal / Alanyl-tRNA synthetase, class IIc, core domain / tRNA synthetases class II (A) / Alanyl-transfer RNA synthetases family profile. / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl/alanyl tRNA synthetase, SAD ...Alanine-tRNA ligase, eukaryota/bacteria / Alanine-tRNA ligase, class IIc / Alanine-tRNA ligase, class IIc, anti-codon-binding domain superfamily / : / Alanyl-tRNA synthetase, class IIc, N-terminal / Alanyl-tRNA synthetase, class IIc, core domain / tRNA synthetases class II (A) / Alanyl-transfer RNA synthetases family profile. / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / DHHA1 domain / DHHA1 domain / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Translation protein, beta-barrel domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
'5'-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE / Alanine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsZhou, H. / He, W. / Yang, X.L.
CitationJournal: To Be Published
Title: Crystal structure of human AlaRS catalytic domain with R329H mutation
Authors: Yang, X.L.
History
DepositionDec 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Sep 27, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)108,22614
Polymers106,5902
Non-polymers1,63612
Water14,592810
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A: Alanine--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1137
Polymers53,2951
Non-polymers8186
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alanine--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1137
Polymers53,2951
Non-polymers8186
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.848, 121.172, 68.012
Angle α, β, γ (deg.)90.000, 118.470, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Alanine--tRNA ligase, cytoplasmic / Alanyl-tRNA synthetase / AlaRS / Renal carcinoma antigen NY-REN-42


Mass: 53295.145 Da / Num. of mol.: 2 / Fragment: Catalytic domain / Mutation: R329H
Source method: isolated from a genetically manipulated source
Details: C-ter fragment got degraded during crystallization / Source: (gene. exp.) Homo sapiens (human) / Gene: AARS / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P49588, alanine-tRNA ligase

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Non-polymers , 5 types, 822 molecules

#2: Chemical ChemComp-A5A / '5'-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE


Mass: 417.398 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H19N7O7S
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 810 / 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: 2.3 Å3/Da / Density % sol: 46.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: PEG3350

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.38→50 Å / Num. obs: 185858 / % possible obs: 98.3 % / Redundancy: 3.6 % / Net I/σ(I): 29
Reflection shellResolution: 1.38→1.4 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 2.6 / Num. unique all: 7807 / % possible all: 82.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HXU

3hxu


Resolution: 1.38→33.96 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.062 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2139 9339 5 %RANDOM
Rwork0.1826 176334 --
obs0.1841 176334 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.33 Å2 / Biso mean: 20.396 Å2 / Biso min: 8.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.26 Å2
2--0.25 Å2-0 Å2
3----0.06 Å2
Refinement stepCycle: final / Resolution: 1.38→33.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6008 0 102 810 6920
Biso mean--18.19 34.77 -
Num. residues----762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0196530
X-RAY DIFFRACTIONr_angle_refined_deg1.1181.9768914
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8125850
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.56524.321324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.416151125
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0971545
X-RAY DIFFRACTIONr_chiral_restr0.0770.2982
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215041
X-RAY DIFFRACTIONr_rigid_bond_restr1.53436530
X-RAY DIFFRACTIONr_sphericity_free32.2185200
X-RAY DIFFRACTIONr_sphericity_bonded10.32456967
LS refinement shellResolution: 1.379→1.415 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 581 -
Rwork0.258 11089 -
all-11670 -
obs--83.75 %

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