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- PDB-3hxz: Crystal Structure of catalytic fragment of E. coli AlaRS G237A in... -

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Basic information

Entry
Database: PDB / ID: 3hxz
TitleCrystal Structure of catalytic fragment of E. coli AlaRS G237A in complex with AlaSA
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) deacylase activity / peptide lactyltransferase (ATP-dependent) activity / alanyl-tRNA aminoacylation / Ligases / alanine-tRNA ligase / alanine-tRNA ligase activity / aminoacyl-tRNA deacylase activity / DNA-binding transcription repressor activity / tRNA binding / negative regulation of DNA-templated transcription ...Ser-tRNA(Ala) deacylase activity / peptide lactyltransferase (ATP-dependent) activity / alanyl-tRNA aminoacylation / Ligases / alanine-tRNA ligase / alanine-tRNA ligase activity / aminoacyl-tRNA deacylase 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
'5'-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE / 2-HYDROXYETHYL DISULFIDE / Alanine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.99 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
B: Alanyl-tRNA synthetase
C: Alanyl-tRNA synthetase
D: Alanyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,60920
Polymers199,7524
Non-polymers3,85716
Water43,7042426
1
A: Alanyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1416
Polymers49,9381
Non-polymers1,2035
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alanyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1416
Polymers49,9381
Non-polymers1,2035
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Alanyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6644
Polymers49,9381
Non-polymers7263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Alanyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6644
Polymers49,9381
Non-polymers7263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)162.928, 162.186, 125.713
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Alanyl-tRNA synthetase / Alanine-tRNA ligase / AlaRS


Mass: 49938.082 Da / Num. of mol.: 4 / Fragment: N-terminal Catalytic fragment residues 2-442 / Mutation: H104L, Q108L, E112L, G237A
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-A5A / '5'-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE


Mass: 417.398 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H19N7O7S
#3: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


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


Mass: 154.251 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2426 / 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: 70.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 30% PEG400, 0.1 M HEPES pH 7.8, vapor diffusion, sitting drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97971 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97971 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 218463 / % possible obs: 98.4 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 10.315
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
1.99-2.073.20.39993.8
2.07-2.153.60.32697.9
2.15-2.253.70.24898
2.25-2.373.80.19798.3
2.37-2.523.90.16398.6
2.52-2.7140.13599.1
2.71-2.994.10.10899.4
2.99-3.424.20.09299.8
3.42-4.314.30.07799.8
4.31-504.30.04799.6

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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: 1.99→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.691 / SU ML: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.201 10963 5 %
Rwork0.167 --
obs0.169 218445 98.1 %
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 28.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å2-0.04 Å2
2--0.06 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.99→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14068 0 236 2426 16730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.02214861
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8331.9620133
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5251830
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.57923.558773
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.471152483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.76415133
X-RAY DIFFRACTIONr_chiral_restr0.0580.22125
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0211521
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1890.37594
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.510152
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.53159
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.385
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.5131
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.70829132
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.017314260
X-RAY DIFFRACTIONr_scbond_it5.54626464
X-RAY DIFFRACTIONr_scangle_it7.55135838
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.99→2.04 Å
RfactorNum. reflection% reflection
Rfree0.283 719 -
Rwork0.226 13647 -
obs--87.65 %

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