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- PDB-1v7o: Alanyl-tRNA synthetase editing domain homologue protein from Pyro... -

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Basic information

Entry
Database: PDB / ID: 1v7o
TitleAlanyl-tRNA synthetase editing domain homologue protein from Pyrococcus horikoshii
Componentsalanyl-tRNA synthetase
KeywordsHYDROLASE
Function / homology
Function and homology information


aminoacyl-tRNA ligase activity / tRNA aminoacylation / aminoacyl-tRNA deacylase activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
: / Replication Terminator Protein; Chain A, domain 2 - #20 / Threonyl-trna Synthetase; Chain A, domain 2 / Replication Terminator Protein; Chain A, domain 2 / Threonyl-tRNA Synthetase; Chain A, domain 2 / Threonyl/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Alanyl-tRNA editing protein AlaX-S
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.62 Å
AuthorsOkada, A. / Yao, M. / Sokabe, M. / Tanaka, I.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Molecular basis of alanine discrimination in editing site
Authors: Sokabe, M. / Okada, A. / Yao, M. / Nakashima, T. / Tanaka, I.
History
DepositionDec 18, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: alanyl-tRNA synthetase
B: alanyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)38,7902
Polymers38,7902
Non-polymers00
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.191, 88.741, 110.122
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


Mass: 19394.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH0574 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: O58307
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: PEG 4000, Tris, MPD, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 MTris-HCl1reservoirpH8.6
224 %(w/v)PEG40001reservoir
33 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9797, 0.9800, 0.9000
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 18, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
20.981
30.91
ReflectionResolution: 2.62→50 Å / Num. obs: 10576 / % possible obs: 99.7 % / Redundancy: 6.3 % / Biso Wilson estimate: 52.5 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 9.2
Reflection shellResolution: 2.62→2.71 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.394 / Num. unique all: 1007 / % possible all: 99.6
Reflection
*PLUS
Lowest resolution: 50 Å
Reflection shell
*PLUS
% possible obs: 99.6 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
SHARPphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.62→15 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 681 6.5 %random
Rwork0.235 ---
all-10576 --
obs-10472 99.2 %-
Solvent computationSolvent model: throughout / Bsol: 41.1 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 51.82 Å2
Baniso -1Baniso -2Baniso -3
1--7.8 Å20 Å20 Å2
2--4.4 Å20 Å2
3---3.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.456 Å0.363 Å
Luzzati d res low-5 Å
Luzzati sigma a0.494 Å0.331 Å
Refinement stepCycle: LAST / Resolution: 2.62→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2513 0 0 107 2620
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.42
X-RAY DIFFRACTIONc_dihedral_angle_d23.869
X-RAY DIFFRACTIONc_improper_angle_d0.952
X-RAY DIFFRACTIONc_mcbond_it1.7
X-RAY DIFFRACTIONc_mcangle_it2.95
X-RAY DIFFRACTIONc_scbond_it2.16
X-RAY DIFFRACTIONc_scangle_it3.35
Refine LS restraints NCSNCS model details: RESTRAINT FOR MAIN CHAIN / Weight position: 3
LS refinement shellResolution: 2.62→2.82 Å
RfactorNum. reflection% reflection
Rfree0.334 88 4.3 %
Rwork0.293 1887 -
obs-1975 96.3 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top
Refinement
*PLUS
Lowest resolution: 15 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.869
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.952

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