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- PDB-4ah6: Human mitochondrial aspartyl-tRNA synthetase -

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Basic information

Entry
Database: PDB / ID: 4ah6
TitleHuman mitochondrial aspartyl-tRNA synthetase
ComponentsASPARTATE--TRNA LIGASE, MITOCHONDRIAL
KeywordsLIGASE
Function / homology
Function and homology information


mitochondrial asparaginyl-tRNA aminoacylation / aspartate-tRNA(Asn) ligase activity / aspartate-tRNA ligase / aspartate-tRNA ligase activity / tRNA aminoacylation / Mitochondrial tRNA aminoacylation / tRNA aminoacylation for protein translation / tRNA binding / mitochondrial matrix / protein homodimerization activity ...mitochondrial asparaginyl-tRNA aminoacylation / aspartate-tRNA(Asn) ligase activity / aspartate-tRNA ligase / aspartate-tRNA ligase activity / tRNA aminoacylation / Mitochondrial tRNA aminoacylation / tRNA aminoacylation for protein translation / tRNA binding / mitochondrial matrix / protein homodimerization activity / mitochondrion / nucleoplasm / ATP binding
Similarity search - Function
GAD-like domain / Aspartate-tRNA ligase, type 1 / GAD domain / GAD domain / GAD-like domain superfamily / Aspartyl/Asparaginyl-tRNA synthetase, class IIb / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain ...GAD-like domain / Aspartate-tRNA ligase, type 1 / GAD domain / GAD domain / GAD-like domain superfamily / Aspartyl/Asparaginyl-tRNA synthetase, class IIb / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Gyrase A; domain 2 / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Aspartate--tRNA ligase, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsNeuenfeldt, A. / Sissler, M. / Lorber, B. / Florentz, C. / Sauter, C.
Citation
Journal: Nucleic Acids Res. / Year: 2013
Title: Thermodynamic Properties Distinguish Human Mitochondrial Aspartyl-tRNA Synthetase from Bacterial Homolog with Same 3D Architecture
Authors: Ennifar, E. / Florentz, C. / Gaudry, A. / Lorber, B. / Neuenfeldt, A. / Sauter, C. / Sissler, M.
#1: Journal: Biochimie / Year: 2009
Title: Peculiar Inhibition of Human Mitochondrial Aspartyl-tRNA Synthetase by Adenylate Analogs.
Authors: Messmer, M. / Blais, S.P. / Balg, C. / Chenevert, R. / Grenier, L. / Lague, P. / Sauter, C. / Sissler, M. / Giege, R. / Lapointe, J. / Florentz, C.
#2: Journal: J.Biol.Chem. / Year: 2006
Title: Loss of a Primordial Identity Element for a Mammalian Mitochondrial Aminoacylation System.
Authors: Fender, A. / Sauter, C. / Messmer, M. / Putz, J. / Giege, R. / Florentz, C. / Sissler, M.
History
DepositionFeb 3, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ASPARTATE--TRNA LIGASE, MITOCHONDRIAL
B: ASPARTATE--TRNA LIGASE, MITOCHONDRIAL
C: ASPARTATE--TRNA LIGASE, MITOCHONDRIAL
D: ASPARTATE--TRNA LIGASE, MITOCHONDRIAL


Theoretical massNumber of molelcules
Total (without water)281,5114
Polymers281,5114
Non-polymers00
Water0
1
A: ASPARTATE--TRNA LIGASE, MITOCHONDRIAL
B: ASPARTATE--TRNA LIGASE, MITOCHONDRIAL


Theoretical massNumber of molelcules
Total (without water)140,7562
Polymers140,7562
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11020 Å2
ΔGint-50.2 kcal/mol
Surface area51120 Å2
MethodPISA
2
C: ASPARTATE--TRNA LIGASE, MITOCHONDRIAL
D: ASPARTATE--TRNA LIGASE, MITOCHONDRIAL


Theoretical massNumber of molelcules
Total (without water)140,7562
Polymers140,7562
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10990 Å2
ΔGint-50.3 kcal/mol
Surface area51130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.400, 82.600, 146.300
Angle α, β, γ (deg.)90.00, 100.40, 90.00
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42
13
23
33
43
14
24
34
44
15
25
16
26

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND RESID 42:152
211CHAIN B AND RESID 42:152
311CHAIN C AND RESID 42:152
411CHAIN D AND RESID 42:152
112CHAIN A AND RESID 153:166
212CHAIN B AND RESID 153:166
312CHAIN C AND RESID 153:166
412CHAIN D AND RESID 153:166
113CHAIN B AND (RESID 167:263 OR RESID 281:336 OR RESID 479:630)
213CHAIN A AND (RESID 167:263 OR RESID 281:336 OR RESID 479:630)
313CHAIN C AND (RESID 167:263 OR RESID 281:336 OR RESID 479:630)
413CHAIN D AND (RESID 167:263 OR RESID 281:336 OR RESID 479:630)
114CHAIN A AND RESID 339:473
214CHAIN B AND RESID 339:473
314CHAIN C AND RESID 339:473
414CHAIN D AND RESID 339:473
115CHAIN A AND RESID 264:280
215CHAIN C AND RESID 264:280
116CHAIN B AND RESID 264:280
216CHAIN D AND RESID 264:280

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
ASPARTATE--TRNA LIGASE, MITOCHONDRIAL / ASPARTYL-TRNA SYNTHETASE / ASPRS / DRS


Mass: 70377.773 Da / Num. of mol.: 4 / Fragment: RESIDUES 41-645
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PDEST / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA 2 / References: UniProt: Q6PI48, aspartate-tRNA ligase
Sequence detailsTHE CONSTRUCT CORRESPONDS TO THE PREDICTED MATURE MITOCHONDRIAL ENZYME WHICH STARTS AT RESIDUE 41. ...THE CONSTRUCT CORRESPONDS TO THE PREDICTED MATURE MITOCHONDRIAL ENZYME WHICH STARTS AT RESIDUE 41. MET 40 WAS ADDED FOR EXPRESSION AS WELL AS A C-TERMINAL TAG (VMYLEHHHHHH)

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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: 3.25 Å3/Da / Density % sol: 62 %
Description: DEN REFINEMENT AS IMPLEMENTED IN CNS 1.3 WAS USED TO FIT ASPRS INSERTION DOMAINS INTO THE DENSITY.
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.5
Details: SITTING DROPLETS WERE PREPARED BY MIXING 0.5 UL HSADRS2 AT 10.6 MG/ML (IN 50 MM HEPES-NA PH 7.5, 150 MM NACL, 0.1 MM EDTA, 10% (V/V) GLYCEROL AND 1 MM DTT) WITH 0.5 UL BOTTOM PHASE OF A ...Details: SITTING DROPLETS WERE PREPARED BY MIXING 0.5 UL HSADRS2 AT 10.6 MG/ML (IN 50 MM HEPES-NA PH 7.5, 150 MM NACL, 0.1 MM EDTA, 10% (V/V) GLYCEROL AND 1 MM DTT) WITH 0.5 UL BOTTOM PHASE OF A BIPHASIC MIXTURE OF 50 MM BIS-TRIS PH 5.5, 20% (M/V) PEG-3350 AND 1 M AMMONIUM SULFATE AND EQUILIBRATED BY VAPOR DIFFUSION OVER 50 UL OF THE LATTER SOLUTION.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.7→89 Å / Num. obs: 35768 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 88.02 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 9.4
Reflection shellResolution: 3.7→3.8 Å / Redundancy: 4 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.1 / % possible all: 91.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HOMOLOGY MODEL BASED ON PDB ENTRY 1C0A

1c0a


Resolution: 3.7→29.916 Å / SU ML: 0.49 / σ(F): 2 / Phase error: 29.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2801 1780 5 %
Rwork0.2191 --
obs0.2222 35680 98.82 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 108.2 Å2
Refinement stepCycle: LAST / Resolution: 3.7→29.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18840 0 0 0 18840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00519276
X-RAY DIFFRACTIONf_angle_d1.08426116
X-RAY DIFFRACTIONf_dihedral_angle_d15.1457348
X-RAY DIFFRACTIONf_chiral_restr0.082896
X-RAY DIFFRACTIONf_plane_restr0.0053412
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A854X-RAY DIFFRACTIONPOSITIONAL
12B854X-RAY DIFFRACTIONPOSITIONAL0.032
13C854X-RAY DIFFRACTIONPOSITIONAL0.029
14D854X-RAY DIFFRACTIONPOSITIONAL0.031
21A121X-RAY DIFFRACTIONPOSITIONAL
22B121X-RAY DIFFRACTIONPOSITIONAL0.134
23C121X-RAY DIFFRACTIONPOSITIONAL0.008
24D121X-RAY DIFFRACTIONPOSITIONAL0.191
31B2457X-RAY DIFFRACTIONPOSITIONAL
32A2457X-RAY DIFFRACTIONPOSITIONAL0.071
33C2457X-RAY DIFFRACTIONPOSITIONAL0.059
34D2457X-RAY DIFFRACTIONPOSITIONAL0.039
41A1075X-RAY DIFFRACTIONPOSITIONAL
42B1075X-RAY DIFFRACTIONPOSITIONAL0.15
43C1075X-RAY DIFFRACTIONPOSITIONAL0.113
44D1075X-RAY DIFFRACTIONPOSITIONAL0.147
51A145X-RAY DIFFRACTIONPOSITIONAL
52C145X-RAY DIFFRACTIONPOSITIONAL0.01
61B145X-RAY DIFFRACTIONPOSITIONAL
62D145X-RAY DIFFRACTIONPOSITIONAL0.053
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7-3.79990.34631230.29742370X-RAY DIFFRACTION91
3.7999-3.91150.38411380.2812622X-RAY DIFFRACTION99
3.9115-4.03740.32891350.25032573X-RAY DIFFRACTION99
4.0374-4.18140.31651380.24682623X-RAY DIFFRACTION99
4.1814-4.34830.2771370.23142622X-RAY DIFFRACTION99
4.3483-4.54560.28451350.1982568X-RAY DIFFRACTION99
4.5456-4.78430.25381370.192604X-RAY DIFFRACTION99
4.7843-5.08270.24881370.19312616X-RAY DIFFRACTION99
5.0827-5.47290.24761390.19892639X-RAY DIFFRACTION100
5.4729-6.01960.30571380.22222618X-RAY DIFFRACTION100
6.0196-6.88140.30281400.22582667X-RAY DIFFRACTION100
6.8814-8.63520.25651400.21192643X-RAY DIFFRACTION100
8.6352-29.91710.24081430.19982735X-RAY DIFFRACTION99

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