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- PDB-1riq: The crystal structure of the catalytic fragment of the alanyl-tRN... -

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Basic information

Entry
Database: PDB / ID: 1riq
TitleThe crystal structure of the catalytic fragment of the alanyl-tRNA synthetase
ComponentsAlanyl-tRNA synthetase
KeywordsLIGASE / beta sheet and flanking helices / class II aminoacyl-tRNA synthetase / helix-loop-helix motif
Function / homology
Function and homology information


alanine-tRNA ligase / alanine-tRNA ligase activity / alanyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / tRNA binding / zinc ion binding / ATP 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 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
Alanine--tRNA ligase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.14 Å
AuthorsSwairjo, M.A. / Otero, F.J. / Yang, X.-L. / Lovato, M.A. / Skene, R.J. / McRee, D.E. / Ribas de Pouplana, L. / Schimmel, P.
CitationJournal: Mol.Cell / Year: 2004
Title: Alanyl-tRNA Synthetase Crystal Structure and Design for Acceptor-Stem Recognition
Authors: Swairjo, M.A. / Otero, F.J. / Yang, X.-L. / Lovato, M.A. / Skene, R.J. / McRee, D.E. / Ribas De Pouplana, L. / Schimmel, P.
History
DepositionNov 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alanyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)54,1471
Polymers54,1471
Non-polymers00
Water6,053336
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.890, 74.890, 179.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 54147.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: ALAS, AQ_1293 / Plasmid: pET20b+ / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: O67323, alanine-tRNA ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.33 Å3/Da / Density % sol: 47.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: PEG 5000mme, NaCl, Tris, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9793, 0.9795, 1.0332
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 3, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97951
31.03321
ReflectionResolution: 2.1→50 Å / Num. all: 26377 / Num. obs: 26377 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.081 / Rsym value: 0.08 / Net I/σ(I): 13.6
Reflection shellResolution: 2.11→2.19 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 13.1 / Num. unique all: 5050 / Rsym value: 0.37 / % possible all: 89.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SHARPphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.14→50 Å / Isotropic thermal model: isotropic / Cross valid method: throuhgout / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2514 2627 -random
Rwork0.2069 ---
all0.2069 26377 --
obs0.2069 26377 100 %-
Displacement parametersBiso mean: 37 Å2
Baniso -1Baniso -2Baniso -3
1--1.022 Å20 Å20 Å2
2---1.022 Å20 Å2
3---2.044 Å2
Refinement stepCycle: LAST / Resolution: 2.14→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3641 0 0 336 3977
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0109
X-RAY DIFFRACTIONc_angle_d1.2705
X-RAY DIFFRACTIONc_mcbond_it1.0891.5
X-RAY DIFFRACTIONc_mcangle_it1.612
X-RAY DIFFRACTIONc_scbond_it2.3172
X-RAY DIFFRACTIONc_scangle_it3.1962.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.topprotein_rep.param
X-RAY DIFFRACTION2dna-rna.topdna-rna_rep.param
X-RAY DIFFRACTION3water.topwater_rep.param
X-RAY DIFFRACTION4ion.topion.param

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