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- PDB-3g98: Crystal Structure of the C-Ala domain from Aquifex aeolicus alany... -

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Basic information

Entry
Database: PDB / ID: 3g98
TitleCrystal Structure of the C-Ala domain from Aquifex aeolicus alanyl-tRNA synthetase
ComponentsAlanyl-tRNA synthetase
KeywordsLIGASE / alpha and beta fold / Aminoacyl-tRNA synthetase / ATP-binding / Cytoplasm / Nucleotide-binding / Protein biosynthesis
Function / homology
Function and homology information


alanine-tRNA ligase / alanine-tRNA ligase activity / alanyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / tRNA binding / negative regulation of DNA-templated transcription / zinc ion binding / ATP binding / cytosol
Similarity search - Function
Diaminopimelate Epimerase; Chain A, domain 1 - #40 / 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 ...Diaminopimelate Epimerase; Chain A, domain 1 - #40 / 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 / Diaminopimelate Epimerase; Chain A, domain 1 / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Translation protein, beta-barrel domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Alanine--tRNA ligase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsGuo, M. / Yang, X.L. / Schimmel, P.
CitationJournal: Science / Year: 2009
Title: The C-Ala domain brings together editing and aminoacylation functions on one tRNA.
Authors: Guo, M. / Chong, Y.E. / Beebe, K. / Shapiro, R. / Yang, X.L. / Schimmel, P.
History
DepositionFeb 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)24,3242
Polymers24,3242
Non-polymers00
Water2,504139
1
A: Alanyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)12,1621
Polymers12,1621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alanyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)12,1621
Polymers12,1621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.740, 54.506, 66.256
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 12161.997 Da / Num. of mol.: 2 / Fragment: UNP residues 758-867
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: alaS / Plasmid: pET20b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 CodonPlus / References: UniProt: O67323, alanine-tRNA ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 1.88 Å3/Da / Density % sol: 34.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 30% PEG6000, 100 mM MES, 1 M LiCl, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 6, 2007
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 16315 / Num. obs: 16087 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 11.4 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 46.8
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1375 / Rsym value: 0.405 / % possible all: 86

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SOLVEphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.85→40.28 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 6.216 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.17 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21871 808 5 %RANDOM
Rwork0.18423 ---
all0.216 16315 --
obs0.18598 15234 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.535 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20 Å20 Å2
2---0.7 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.85→40.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1718 0 0 139 1857
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221738
X-RAY DIFFRACTIONr_angle_refined_deg0.9841.9932322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4745224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.15225.12878
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.77715350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4271512
X-RAY DIFFRACTIONr_chiral_restr0.0710.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021286
X-RAY DIFFRACTIONr_nbd_refined0.2350.3840
X-RAY DIFFRACTIONr_nbtor_refined0.3210.51178
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2320.5222
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.353
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2610.525
X-RAY DIFFRACTIONr_mcbond_it5.47431128
X-RAY DIFFRACTIONr_mcangle_it6.24631746
X-RAY DIFFRACTIONr_scbond_it7.3572660
X-RAY DIFFRACTIONr_scangle_it10.1313574
LS refinement shellResolution: 1.85→1.901 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 33 -
Rwork0.285 1023 -
obs--90.1 %

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