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- PDB-1b8a: ASPARTYL-TRNA SYNTHETASE -

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Entry
Database: PDB / ID: 1b8a
TitleASPARTYL-TRNA SYNTHETASE
ComponentsPROTEIN (ASPARTYL-TRNA SYNTHETASE)
KeywordsLIGASE / SYNTHETASE / TRNA LIGASE
Function / homologyAminoacyl-tRNA synthetase, class II (D/K/N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / Aminoacyl-transfer RNA synthetases class-II family profile. / OB-fold nucleic acid binding domain / tRNA synthetases class II (D, K and N) / Nucleic acid-binding, OB-fold / Aminoacyl-tRNA synthetase, class II / Aspartate-tRNA synthetase, type 2 / Aspartyl/Asparaginyl-tRNA synthetase, class IIb / aspartate-tRNA ligase ...Aminoacyl-tRNA synthetase, class II (D/K/N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / Aminoacyl-transfer RNA synthetases class-II family profile. / OB-fold nucleic acid binding domain / tRNA synthetases class II (D, K and N) / Nucleic acid-binding, OB-fold / Aminoacyl-tRNA synthetase, class II / Aspartate-tRNA synthetase, type 2 / Aspartyl/Asparaginyl-tRNA synthetase, class IIb / aspartate-tRNA ligase / aspartyl-tRNA aminoacylation / aspartate-tRNA ligase activity / aminoacyl-tRNA synthetase multienzyme complex / magnesium ion binding / RNA binding / ATP binding / cytosol / Aspartate--tRNA(Asp) ligase
Function and homology information
Specimen sourceThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 1.9 Å resolution
AuthorsSchmitt, E. / Moulinier, L. / Thierry, J.-C. / Moras, D.
CitationJournal: EMBO J. / Year: 1998
Title: Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation.
Authors: Schmitt, E. / Moulinier, L. / Fujiwara, S. / Imanaka, T. / Thierry, J.C. / Moras, D.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 27, 1999 / Release: Feb 2, 1999
RevisionDateData content typeGroupCategoryItemProviderType
1.0Feb 2, 1999Structure modelrepositoryInitial release
1.1Apr 26, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelSource and taxonomy / Version format compliance
1.3Oct 4, 2017Structure modelRefinement descriptionsoftware_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (ASPARTYL-TRNA SYNTHETASE)
B: PROTEIN (ASPARTYL-TRNA SYNTHETASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,30510
Polyers101,9612
Non-polymers1,3448
Water22,1581230
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)11420
ΔGint (kcal/M)-86
Surface area (Å2)33620
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)124.800, 125.000, 87.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP 21 21 2

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Components

#1: Protein/peptide PROTEIN (ASPARTYL-TRNA SYNTHETASE) / EC 6.1.1.12 / ASPARTYL TRNA LIGASE


Mass: 50980.398 Da / Num. of mol.: 2 / Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Genus: Thermococcus / Species: Thermococcus kodakarensis / Strain: KOD1 / Cellular location: CYTOPLASM / Gene: ASPS / Plasmid name: PUC18F / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: Q52428, aspartate-tRNA ligase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Formula: Mn / Manganese
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1230 / Formula: H2O / Water

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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: 3.33 / Density percent sol: 63.09 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Temp: 24 ℃ / Method: vapor diffusion, hanging drop
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
14 mg/mlprotein1drop
210 mMTris-HCl1reservoir
310 mM2-mercaptoethanol1reservoir
4100 mM1reservoirKCl
532-38 %ethylene glycol1reservoir

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Data collection

DiffractionMean temperature: 120 kelvins
SourceSource: SYNCHROTRON / Type: LURE BEAMLINE DW32 / Synchrotron site: LURE / Beamline: DW32 / Wavelength: 1
DetectorType: MARRESEARCH / Details: MIRRORS / Detector: IMAGE PLATE
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 8.2 Å2 / D resolution high: 1.9 Å / D resolution low: 15 Å / Number obs: 3916674 / Observed criterion sigma I: 2 / Rsym value: 5 / Redundancy: 3.8 % / Percent possible obs: 96
Reflection
*PLUS
Number obs: 105560 / Number measured all: 3916674 / Rmerge I obs: 0.05
Reflection shell
*PLUS
Rmerge I obs: 0.269

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.4refinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ASZ
R Free selection details: RANDOM / Data cutoff high rms absF: 2674497.32 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 0
Solvent computationSolvent model details: FLAT MODEL / Solvent model param bsol: 50.7 / Solvent model param ksol: 0.37
Displacement parametersB iso mean: 19 Å2 / Aniso B11: 6.12 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: -2.26 Å2 / Aniso B23: 0 Å2 / Aniso B33: -3.87 Å2
Least-squares processR factor R free: 0.202 / R factor R free error: 0.003 / R factor R work: 0.168 / Highest resolution: 1.9 Å / Lowest resolution: 15 Å / Number reflection R free: 5102 / Number reflection all: 101060 / Number reflection obs: 101060 / Percent reflection R free: 5 / Percent reflection obs: 93.9
Refine analyzeLuzzati coordinate error free: 0.21 Å / Luzzati coordinate error obs: 0.17 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a free: 0.17 Å / Luzzati sigma a obs: 0.13 Å
Refine hist #LASTHighest resolution: 1.9 Å / Lowest resolution: 15 Å
Number of atoms included #LASTProtein: 7188 / Nucleic acid: 0 / Ligand: 68 / Solvent: 1230 / Total: 8486
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.05
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it0.881.50
X-RAY DIFFRACTIONx_mcangle_it1.432.00
X-RAY DIFFRACTIONx_scbond_it1.492.00
X-RAY DIFFRACTIONx_scangle_it2.242.50
Refine LS shellHighest resolution: 1.9 Å / R factor R free: 0.239 / R factor R free error: 0.009 / R factor R work: 0.2 / Lowest resolution: 2.02 Å / Number reflection R free: 784 / Number reflection R work: 14554 / Total number of bins used: 6 / Percent reflection R free: 5.1 / Percent reflection obs: 86.6
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNAMULTLUC.PARAMDNA-RNA_OLD.TOP
X-RAY DIFFRACTION3LIGAND.PARAMWATER.TOP
X-RAY DIFFRACTION4PARAM19.IONLIGAND.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.05
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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