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- PDB-2zvf: Crystal structure of Archaeoglobus fulgidus alanyl-tRNA synthetas... -

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Basic information

Entry
Database: PDB / ID: 2zvf
TitleCrystal structure of Archaeoglobus fulgidus alanyl-tRNA synthetase C-terminal dimerization domain
ComponentsAlanyl-tRNA synthetase
KeywordsLIGASE / Alanyl-tRNA synthetase / C-terminal / oligomerization domain / Aminoacyl-tRNA synthetase / ATP-binding / Cytoplasm / Nucleotide-binding / Protein biosynthesis / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
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 / identical protein binding / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #550 / Diaminopimelate Epimerase; Chain A, domain 1 - #40 / Alanine-tRNA ligase, archaea / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #550 / Diaminopimelate Epimerase; Chain A, domain 1 - #40 / Alanine-tRNA ligase, archaea / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Helix non-globular / Special / Translation protein, beta-barrel domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Alanine--tRNA ligase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsNaganuma, M. / Sekine, S. / Fukunaga, R. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Unique protein architecture of alanyl-tRNA synthetase for aminoacylation, editing, and dimerization.
Authors: Naganuma, M. / Sekine, S. / Fukunaga, R. / Yokoyama, S.
History
DepositionNov 6, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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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
E: Alanyl-tRNA synthetase
F: Alanyl-tRNA synthetase
G: Alanyl-tRNA synthetase
H: Alanyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,59614
Polymers157,0208
Non-polymers5766
Water18010
1
A: Alanyl-tRNA synthetase
B: Alanyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4474
Polymers39,2552
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-58 kcal/mol
Surface area18350 Å2
MethodPISA
2
C: Alanyl-tRNA synthetase
D: Alanyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4474
Polymers39,2552
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-61 kcal/mol
Surface area18560 Å2
MethodPISA
3
E: Alanyl-tRNA synthetase
F: Alanyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3513
Polymers39,2552
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-48 kcal/mol
Surface area18570 Å2
MethodPISA
4
G: Alanyl-tRNA synthetase
H: Alanyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3513
Polymers39,2552
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-47 kcal/mol
Surface area18570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.109, 131.714, 138.823
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

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Components

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


Mass: 19627.453 Da / Num. of mol.: 8 / Fragment: C-terminal domain (residues 737-906)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF_2255, alaS / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): rosseta2 / References: UniProt: O28029, alanine-tRNA ligase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.61 Å3/Da / Density % sol: 65.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 1.6M ammonium sulfate, 7.5% hexanediol, pH 8.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 11, 2006 / Details: monochrometer
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.2→50.78 Å / Num. all: 39055 / Num. obs: 38548 / % possible obs: 98.7 % / Observed criterion σ(F): -1 / Redundancy: 9.7 % / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 18.4
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 2.18 / Num. unique all: 3520 / Rsym value: 0.386 / % possible all: 91.3

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 3.2→50 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 89629.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1898 5 %RANDOM
Rwork0.205 ---
obs0.205 37899 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 69.5292 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 83.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20 Å2
2--0.21 Å20 Å2
3----0.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.71 Å0.61 Å
Refinement stepCycle: LAST / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10705 0 30 10 10745
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it7.51.5
X-RAY DIFFRACTIONc_mcangle_it12.212
X-RAY DIFFRACTIONc_scbond_it11.442
X-RAY DIFFRACTIONc_scangle_it17.032.5
LS refinement shellResolution: 3.2→3.31 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.359 172 4.8 %
Rwork0.311 3384 -
obs-3520 94.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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