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- PDB-1wle: Crystal Structure of mammalian mitochondrial seryl-tRNA synthetas... -

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Basic information

Entry
Database: PDB / ID: 1wle
TitleCrystal Structure of mammalian mitochondrial seryl-tRNA synthetase complexed with seryl-adenylate
ComponentsSeryl-tRNA synthetase
KeywordsLIGASE
Function / homology
Function and homology information


mitochondrial seryl-tRNA aminoacylation / serine-tRNA ligase / serine-tRNA ligase activity / seryl-tRNA aminoacylation / tRNA binding / mitochondrial matrix / mitochondrion / ATP binding / cytosol
Similarity search - Function
Serine-tRNA synthetase, tRNA binding domain / Serine-tRNA ligase, type1 / Serine-tRNA ligase catalytic core domain / Serine-tRNA synthetase, type1, N-terminal domain superfamily / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II ...Serine-tRNA synthetase, tRNA binding domain / Serine-tRNA ligase, type1 / Serine-tRNA ligase catalytic core domain / Serine-tRNA synthetase, type1, N-terminal domain superfamily / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
SERYL ADENYLATE / Serine--tRNA ligase, mitochondrial
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsChimnaronk, S. / Jeppesen, M.G. / Suzuki, T. / Nyborg, J. / Watanabe, K.
Citation
Journal: Embo J. / Year: 2005
Title: Dual-mode recognition of noncanonical tRNAs(Ser) by seryl-tRNA synthetase in mammalian mitochondria
Authors: Chimnaronk, S. / Jeppesen, M.G. / Suzuki, T. / Nyborg, J. / Watanabe, K.
#1: Journal: J.Biol.Chem. / Year: 2000
Title: Characterization and tRNA recognition of mammalian mitochondrial seryl-tRNA synthetase
Authors: Yokogawa, T. / Shimada, N. / Takeuchi, N. / Benkowski, L. / Suzuki, T. / Omori, A. / Ueda, T. / Nishikawa, K. / Spremulli, L.L. / Watanabe, K.
#2: Journal: J.Biol.Chem. / Year: 2001
Title: Dual mode recognition of two isoacceptor tRNAs by mammalian mitochondrial seryl-tRNA synthetase
Authors: Shimada, N. / Suzuki, T. / Watanabe, K.
#3: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2004
Title: Crystallization and preliminary X-ray diffraction study of mammalian mitochondrial seryl-tRNA synthetase
Authors: Chimnaronk, S. / Jeppesen, M.G. / Shimada, N. / Suzuki, T. / Nyborg, J. / Watanabe, K.
History
DepositionJun 25, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Seryl-tRNA synthetase
B: Seryl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,9954
Polymers113,1262
Non-polymers8692
Water11,007611
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8250 Å2
ΔGint-36 kcal/mol
Surface area40740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.864, 230.350, 135.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a homodimer found in the asymmetric unit.

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Components

#1: Protein Seryl-tRNA synthetase / mitochondrial seryl-tRNA synthetase / Serine--tRNA ligase / SerRSmt


Mass: 56563.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: SerRSmt / Plasmid: pET-19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta (Novagen) / References: UniProt: Q9N0F3, serine-tRNA ligase
#2: Chemical ChemComp-SRP / SERYL ADENYLATE


Mass: 434.299 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H19N6O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 611 / 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: 2.8 Å3/Da / Density % sol: 55.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: PEG 8000, lithium sulfate, MES-NaOH, DTT, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8123 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 6, 2003 / Details: Bent mirror
RadiationMonochromator: Triangular / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 1.65→99 Å / Num. all: 145408 / Num. obs: 145408 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -0.3 / Redundancy: 6.3 % / Biso Wilson estimate: 21.206 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 30.7
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 1.8 / Num. unique all: 9594 / % possible all: 96.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1SRY

1sry


Resolution: 1.65→10 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2256 14531 9.7 %RANDOM
Rwork0.21 ---
all-144630 --
obs-144630 96.2 %-
Solvent computationSolvent model: THROUGHOUT / Bsol: 63.3399 Å2 / ksol: 0.483133 e/Å3
Displacement parametersBiso mean: 28.5261 Å2
Baniso -1Baniso -2Baniso -3
1--1.421 Å20 Å20 Å2
2---2.233 Å20 Å2
3---3.654 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.65→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7437 0 58 611 8106
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005175
X-RAY DIFFRACTIONc_angle_deg1.35365
X-RAY DIFFRACTIONc_dihedral_angle_d22.12441
X-RAY DIFFRACTIONc_improper_angle_d0.8152
X-RAY DIFFRACTIONc_mcbond_it1.169
X-RAY DIFFRACTIONc_mcangle_it1.844
X-RAY DIFFRACTIONc_scbond_it1.819
X-RAY DIFFRACTIONc_scangle_it2.756
LS refinement shellResolution: 1.64→1.7 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2895 1420 9.53 %
Rwork0.2777 12400 -
obs-13820 0.9273 %
Xplor fileSerial no: 1 / Param file: SMP.PARAM / Topol file: SMP.TOP

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