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- PDB-5v59: Crystal structure of catalytic fragment of human AlaRS in complex... -

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Basic information

Entry
Database: PDB / ID: 5v59
TitleCrystal structure of catalytic fragment of human AlaRS in complex with Aze-SA
ComponentsAlanine--tRNA ligase, cytoplasmic
KeywordsLIGASE / Aminoacyl-tRNA synthetase / Non-proteinogenic amino acid
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
Chem-8X1 / Alanine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsZhou, H. / Song, Y. / Schimmel, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM23562 United States
CitationJournal: Nat Commun / Year: 2017
Title: Double mimicry evades tRNA synthetase editing by toxic vegetable-sourced non-proteinogenic amino acid.
Authors: Song, Y. / Zhou, H. / Vo, M.N. / Shi, Y. / Nawaz, M.H. / Vargas-Rodriguez, O. / Diedrich, J.K. / Yates, J.R. / Kishi, S. / Musier-Forsyth, K. / Schimmel, P.
History
DepositionMar 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)53,7442
Polymers53,3141
Non-polymers4291
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.330, 67.270, 86.350
Angle α, β, γ (deg.)90.000, 136.230, 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 (UNP residues 1-455)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AARS / Production host: Escherichia coli (E. coli) / References: UniProt: P49588, alanine-tRNA ligase
#2: Chemical ChemComp-8X1 / 5'-O-{[(2S)-azetidine-2-carbonyl]sulfamoyl}adenosine


Mass: 429.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H19N7O7S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.04 Å3/Da / Density % sol: 39.74 %
Crystal growTemperature: 310 K / Method: vapor diffusion / pH: 8 / Details: 25% PEG6000, 100 mM Tris-HCl, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.03→59.734 Å / Num. obs: 27565 / % possible obs: 99.2 % / Redundancy: 3.9 % / Rpim(I) all: 0.034 / Rrim(I) all: 0.069 / Rsym value: 0.06 / Net I/av σ(I): 10.5 / Net I/σ(I): 15.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRpim(I) allRrim(I) allRsym value% possible all
2.03-2.143.70.322.438000.1890.3730.3294.8
2.14-2.273.90.2193.50.1270.2540.219100
2.27-2.433.90.1684.50.0970.1950.168100
2.43-2.6240.1226.10.070.1410.122100
2.62-2.8740.0829.20.0470.0950.082100
2.87-3.2140.05313.70.030.0610.053100
3.21-3.7140.03619.50.020.0410.036100
3.71-4.5440.035170.020.0410.035100
4.54-6.4340.03516.40.020.040.035100
6.43-42.9243.90.02621.10.0150.030.02699.6

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Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4XEM
Resolution: 2.03→59.73 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.925 / SU B: 8.107 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.158
RfactorNum. reflection% reflectionSelection details
Rfree0.2146 1390 5 %RANDOM
Rwork0.1799 ---
obs0.1817 26163 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 67.87 Å2 / Biso mean: 26.974 Å2 / Biso min: 3.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å2-1.12 Å2
2--0.62 Å20 Å2
3----1.5 Å2
Refinement stepCycle: final / Resolution: 2.03→59.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2996 0 29 245 3270
Biso mean--20.63 23.53 -
Num. residues----379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223155
X-RAY DIFFRACTIONr_angle_refined_deg1.2271.9694297
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7165401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.80724.568162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.34515525
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1121521
X-RAY DIFFRACTIONr_chiral_restr0.0720.2466
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212463
LS refinement shellResolution: 2.034→2.087 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 93 -
Rwork0.251 1803 -
all-1896 -
obs--93.08 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.61950.85820.12371.8195-0.171.7358-0.0748-0.0701-0.3075-0.08950.1075-0.0470.1984-0.0337-0.03270.07790.0045-0.0060.0460.03250.0556-12.4958-9.427318.5329
21.22140.0649-0.09171.0861-0.01821.59240.0154-0.02840.0879-0.08240.0210.185-0.1435-0.3133-0.03640.07520.0457-0.01840.08690.02690.0689-22.74262.31139.4731
31.5653-0.1884-0.13443.30040.73252.5598-0.02570.17310.1188-0.2120.0514-0.0866-0.1638-0.0884-0.02570.05610.0079-0.01840.07310.0460.06-16.3936-0.15634.8469
41.34310.49040.07371.21520.531.02-0.022-0.24530.05320.00010.1049-0.1275-0.06030.1672-0.08290.06160.00990.00410.0982-0.03520.02513.58724.352223.5039
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 87
2X-RAY DIFFRACTION2A88 - 169
3X-RAY DIFFRACTION3A170 - 236
4X-RAY DIFFRACTION4A237 - 384

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