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- PDB-3hxw: Crystal Structure of catalytic fragment of E. coli AlaRS in compl... -

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Basic information

Entry
Database: PDB / ID: 3hxw
TitleCrystal Structure of catalytic fragment of E. coli AlaRS in complex with SerSA
ComponentsAlanyl-tRNA synthetaseAlanine—tRNA ligase
KeywordsLIGASE / Aminoacyl-tRNA synthetase / Protein biosynthesis / Nucleotide-binding / amino acid-binding / ATP-binding / Metal-binding / Zinc-finger
Function / homology
Function and homology information


Ser-tRNA(Ala) hydrolase activity / alanine-tRNA ligase / alanine-tRNA ligase activity / alanyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / DNA-binding transcription repressor activity / tRNA binding / negative regulation of DNA-templated transcription / protein homodimerization activity / zinc ion binding ...Ser-tRNA(Ala) hydrolase activity / alanine-tRNA ligase / alanine-tRNA ligase activity / alanyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / DNA-binding transcription repressor activity / tRNA binding / negative regulation of DNA-templated transcription / protein homodimerization activity / zinc ion binding / ATP binding / membrane / identical protein binding / cytosol
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
2-HYDROXYETHYL DISULFIDE / 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE / Alanine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.93 Å
AuthorsGuo, M. / Yang, X.-L. / Schimmel, P.
CitationJournal: Nature / Year: 2009
Title: Paradox of mistranslation of serine for alanine caused by AlaRS recognition dilemma.
Authors: Guo, M. / Chong, Y.E. / Shapiro, R. / Beebe, K. / Yang, X.L. / Schimmel, P.
History
DepositionJun 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alanyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0596
Polymers49,9241
Non-polymers1,1345
Water13,962775
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.858, 114.858, 126.081
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 Alanyl-tRNA synthetase / Alanine—tRNA ligase / Alanine-tRNA ligase / AlaRS


Mass: 49924.055 Da / Num. of mol.: 1 / Fragment: N-terminal Catalytic fragment residues 2-442 / Mutation: H104L, Q108L, E112L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: alaS, lovB, b2697, JW2667 / Plasmid: pET20b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CondonPlus / References: UniProt: P00957, alanine-tRNA ligase
#2: Chemical ChemComp-SSA / 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE


Mass: 433.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H19N7O8S
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-HED / 2-HYDROXYETHYL DISULFIDE


Mass: 154.251 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 775 / 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: 4.16 Å3/Da / Density % sol: 70.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 27% PEG 400, 0.1 M HEPES pH 7.5, vapor diffusion, sitting drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 63820 / % possible obs: 99.9 % / Redundancy: 28.5 % / Rmerge(I) obs: 0.076 / Χ2: 0.89 / Net I/σ(I): 48.194
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.93-225.20.32162090.51498.8
2-2.0828.80.25863100.613100
2.08-2.1729.40.262760.675100
2.17-2.2929.20.17863290.974100
2.29-2.4329.40.12863130.895100
2.43-2.6229.40.10763611.006100
2.62-2.8829.30.08363621.101100
2.88-3.3290.06663951.237100
3.3-4.1628.20.0664870.865100
4.16-5027.10.04367780.95399.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→42.45 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.177 / WRfactor Rwork: 0.153 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.89 / SU B: 2.022 / SU ML: 0.061 / SU R Cruickshank DPI: 0.1 / SU Rfree: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18 3234 5.1 %RANDOM
Rwork0.158 ---
obs0.159 63734 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 114.78 Å2 / Biso mean: 27.338 Å2 / Biso min: 5 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20 Å2
2---0.59 Å20 Å2
3---1.17 Å2
Refine analyzeLuzzati coordinate error obs: 0.167 Å
Refinement stepCycle: LAST / Resolution: 1.93→42.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3516 0 68 775 4359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0223764
X-RAY DIFFRACTIONr_angle_refined_deg0.8651.9645104
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6145470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.79623.538195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.42315636
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5131534
X-RAY DIFFRACTIONr_chiral_restr0.060.2540
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022913
X-RAY DIFFRACTIONr_nbd_refined0.1880.31928
X-RAY DIFFRACTIONr_nbtor_refined0.3190.52582
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.51017
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.341
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.588
X-RAY DIFFRACTIONr_mcbond_it4.07822304
X-RAY DIFFRACTIONr_mcangle_it4.38133599
X-RAY DIFFRACTIONr_scbond_it5.02321626
X-RAY DIFFRACTIONr_scangle_it7.1831490
LS refinement shellResolution: 1.93→1.981 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 236 -
Rwork0.196 4371 -
all-4607 -
obs--98.82 %

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