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

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Basic information

Entry
Database: PDB / ID: 3hxv
TitleCrystal Structure of catalytic fragment of E. coli AlaRS in complex with GlySA
ComponentsAlanyl-tRNA synthetase
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 / Ligases / 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 ...Ser-tRNA(Ala) hydrolase activity / Ligases / 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 / identical protein binding / membrane / 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 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
BETA-MERCAPTOETHANOL / 5'-O-(glycylsulfamoyl)adenosine / 2-HYDROXYETHYL DISULFIDE / 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 1.2Jun 19, 2013Group: Atomic model
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Oct 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 1.5Feb 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)51,1077
Polymers49,9241
Non-polymers1,1836
Water10,773598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.639, 114.639, 125.398
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alanyl-tRNA synthetase / 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

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Non-polymers , 5 types, 604 molecules

#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


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


Mass: 154.251 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Chemical ChemComp-G5A / 5'-O-(glycylsulfamoyl)adenosine


Mass: 403.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H17N7O7S
#5: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 598 / 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: 4.13 Å3/Da / Density % sol: 70.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: 31% PEG 400, 0.1 M HEPES, pH 7.9, 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: 0.9795 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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 58254 / % possible obs: 92 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 35.739
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.93-260.123194.3
2-2.0860.101194.3
2.08-2.176.10.08193.8
2.17-2.296.10.08193.5
2.29-2.436.10.055193
2.43-2.626.20.047192.4
2.62-2.886.20.04191.8
2.88-3.36.20.035190.7
3.3-4.166.20.04189.6
4.16-506.20.023186.7

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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→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.981 / SU ML: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.188 2988 5.1 %
Rwork0.159 --
obs0.161 58211 92 %
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 21.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20 Å2
2---0.32 Å20 Å2
3---0.63 Å2
Refine analyzeLuzzati coordinate error obs: 0.249 Å
Refinement stepCycle: LAST / Resolution: 1.93→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3516 0 70 598 4184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223761
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0631.9645095
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7935467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.17223.487195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.44515637
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9031535
X-RAY DIFFRACTIONr_chiral_restr0.3840.2538
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022908
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.31913
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.52584
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.5824
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.349
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2030.562
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.3522301
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.59633595
X-RAY DIFFRACTIONr_scbond_it5.40621659
X-RAY DIFFRACTIONr_scangle_it7.42531486
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.93→1.98 Å
RfactorNum. reflection% reflection
Rfree0.219 219 -
Rwork0.179 4131 -
obs--94.67 %

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