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- PDB-4xem: Crystal Structure of wild type human AlaRS catalytic domain -

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Basic information

Entry
Database: PDB / ID: 4xem
TitleCrystal Structure of wild type human AlaRS catalytic domain
ComponentsAlanine--tRNA ligase, cytoplasmic
KeywordsLIGASE / tRNA synthetase
Function / homology
Function and homology information


regulation of cytoplasmic translational fidelity / Ser-tRNA(Ala) hydrolase activity / alanine-tRNA ligase / alanine-tRNA ligase activity / alanyl-tRNA aminoacylation / cerebellar Purkinje cell layer development / Cytosolic tRNA aminoacylation / tRNA modification / tRNA aminoacylation for protein translation / aminoacyl-tRNA editing activity ...regulation of cytoplasmic translational fidelity / Ser-tRNA(Ala) hydrolase activity / alanine-tRNA ligase / alanine-tRNA ligase activity / alanyl-tRNA aminoacylation / cerebellar Purkinje cell layer development / Cytosolic tRNA aminoacylation / tRNA modification / tRNA aminoacylation for protein translation / aminoacyl-tRNA editing activity / 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/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl and Alanyl tRNA synthetase second additional domain ...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/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / 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: 1.278 Å
AuthorsZhou, H. / He, W. / Yang, X.L.
CitationJournal: To Be Published
Title: Crystal structure of wild type human AlaRS catalytic domain
Authors: Zhou, H. / Yang, X.L.
History
DepositionDec 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)54,0427
Polymers53,3141
Non-polymers7286
Water8,827490
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.121, 67.131, 75.107
Angle α, β, γ (deg.)90.000, 127.420, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 53314.195 Da / Num. of mol.: 1 / Fragment: Catalytic domain
Source method: isolated from a genetically manipulated source
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
#2: Chemical ChemComp-A5A / '5'-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE


Mass: 417.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H19N7O7S
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 490 / 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: 2.12 Å3/Da / Density % sol: 41.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5 / Details: PEG3350

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.278→50 Å / Num. obs: 109596 / % possible obs: 99.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 35.5
Reflection shellResolution: 1.278→1.38 Å / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 2.9 / Num. unique all: 5498 / % possible all: 99.9

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Processing

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

3hxu


Resolution: 1.278→37.33 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.967 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1787 5511 5 %RANDOM
Rwork0.161 104085 --
obs0.1619 104085 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.8 Å2 / Biso mean: 18.117 Å2 / Biso min: 8.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å2-0 Å2-0.08 Å2
2---0.02 Å2-0 Å2
3----0.19 Å2
Refinement stepCycle: final / Resolution: 1.278→37.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2962 0 48 490 3500
Biso mean--16.14 33.99 -
Num. residues----377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193181
X-RAY DIFFRACTIONr_angle_refined_deg1.0831.9684323
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0335402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.924.444162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.82215528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8531522
X-RAY DIFFRACTIONr_chiral_restr0.0760.2467
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212476
X-RAY DIFFRACTIONr_rigid_bond_restr2.59433181
X-RAY DIFFRACTIONr_sphericity_free32.7385116
X-RAY DIFFRACTIONr_sphericity_bonded8.39153481
LS refinement shellResolution: 1.278→1.311 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 378 -
Rwork0.251 7428 -
all-7806 -
obs--96.13 %

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