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- PDB-9qof: E.coli seryl-tRNA synthetase (Arm deletion mutant) bound to sulph... -

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Basic information

Entry
Database: PDB / ID: 9qof
TitleE.coli seryl-tRNA synthetase (Arm deletion mutant) bound to sulphamoyl seryl-adenylate analogue
ComponentsSerine--tRNA ligase
KeywordsTRANSLATION / aminoacyl-tRNA synthetase / ATP binding
Function / homology
Function and homology information


selenocysteine biosynthetic process / serine-tRNA ligase / serine-tRNA ligase activity / seryl-tRNA aminoacylation / magnesium ion binding / ATP binding / identical protein binding / cytosol
Similarity search - Function
Serine-tRNA synthetase, type1, N-terminal / Seryl-tRNA synthetase N-terminal 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) / 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)
Similarity search - Domain/homology
5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE / Serine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsCusack, S. / Belrhali, H. / Price, S. / Leberman, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Nucleic Acids Res / Year: 1994
Title: Seryl-tRNA synthetase from Escherichia coli,implication of its N-terminal domain in aminoacylation activity and specificity.
Authors: Borel, F. / Vincent, C. / Leberman, R. / Hartlein, M.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
#2: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix
Authors: Liebschner, D. / Afonine, P.V. / Baker, M.L. / Bunkoczi, G. / Chen, V.B. / Croll, T.I. / Hintze, B. / Hung, L.W. / Jain, S. / McCoy, A.J. / Moriarty, N.W. / Oeffner, R.D. / Poon, B.K. / ...Authors: Liebschner, D. / Afonine, P.V. / Baker, M.L. / Bunkoczi, G. / Chen, V.B. / Croll, T.I. / Hintze, B. / Hung, L.W. / Jain, S. / McCoy, A.J. / Moriarty, N.W. / Oeffner, R.D. / Poon, B.K. / Prisant, M.G. / Read, R.J. / Richardson, J.S. / Richardson, D.C. / Sammito, M.D. / Sobolev, O.V. / Stockwell, D.H. / Terwilliger, T.C. / Urzhumtsev, A.G. / Videau, L.L. / Williams, C.J. / Adams, P.D.
#3: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMar 26, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine--tRNA ligase
B: Serine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,9628
Polymers82,8542
Non-polymers1,1086
Water5,062281
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7510 Å2
ΔGint-51 kcal/mol
Surface area28560 Å2
Unit cell
Length a, b, c (Å)132.615, 92.901, 171.691
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Serine--tRNA ligase / Seryl-tRNA synthetase / SerRS / Seryl-tRNA(Ser/Sec) synthetase


Mass: 41427.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Seryl-tRNA synthetase from E. coli arm-deletion mutant. Residues 35-97 deleted and replaced by G
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: serS, b0893, JW0876 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8L1, serine-tRNA ligase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-SSA / 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE


Mass: 433.397 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H19N7O8S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.19 Å3/Da / Density % sol: 61.46 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop
Details: Reservoir solution, 1ml of 40-44% potassium phosphate. Drop, 5 microlitre reservoir + 5 microlitre protein solution. Protein solution, 15 mg/ml protein, 10 mM MgCl2, 1mM DTT, 1 mM NaN3. All ...Details: Reservoir solution, 1ml of 40-44% potassium phosphate. Drop, 5 microlitre reservoir + 5 microlitre protein solution. Protein solution, 15 mg/ml protein, 10 mM MgCl2, 1mM DTT, 1 mM NaN3. All solutions ibuffered with 4mM Tris.HCl at pH 7.5 to 8.2.

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Data collection

DiffractionMean temperature: 283 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.905 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Sep 15, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.905 Å / Relative weight: 1
ReflectionResolution: 2.32→11.99 Å / Num. obs: 45240 / % possible obs: 95.4 % / Redundancy: 3.9 % / Biso Wilson estimate: 27.44 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.7
Reflection shellResolution: 2.32→2.37 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.18 / Num. unique obs: 2478

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→11.99 Å / SU ML: 0.1745 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 16.0598
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.163 2223 5.09 %
Rwork0.1296 41476 -
obs0.1314 43699 95.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.99 Å2
Refinement stepCycle: LAST / Resolution: 2.32→11.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5737 0 70 281 6088
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00725964
X-RAY DIFFRACTIONf_angle_d0.74858090
X-RAY DIFFRACTIONf_chiral_restr0.0476892
X-RAY DIFFRACTIONf_plane_restr0.00791064
X-RAY DIFFRACTIONf_dihedral_angle_d16.09542258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.370.21821390.1572339X-RAY DIFFRACTION88.25
2.37-2.420.22811200.15322409X-RAY DIFFRACTION89.9
2.42-2.480.23571340.15492456X-RAY DIFFRACTION91.13
2.48-2.550.23411360.15662476X-RAY DIFFRACTION92.3
2.55-2.630.19011180.1552520X-RAY DIFFRACTION92.89
2.63-2.710.2161160.15582581X-RAY DIFFRACTION94.3
2.71-2.810.21741380.16022556X-RAY DIFFRACTION94.79
2.81-2.920.19731380.1542610X-RAY DIFFRACTION96.25
2.92-3.050.20921410.14972582X-RAY DIFFRACTION96.53
3.05-3.20.16191430.14442645X-RAY DIFFRACTION97.38
3.2-3.40.17251350.13622678X-RAY DIFFRACTION98.05
3.4-3.660.14531450.12212677X-RAY DIFFRACTION98.33
3.66-4.010.13921440.10922694X-RAY DIFFRACTION98.78
4.01-4.560.11711550.09382706X-RAY DIFFRACTION99.27
4.56-5.650.1211500.09812740X-RAY DIFFRACTION99.14
5.65-11.990.14291710.13552807X-RAY DIFFRACTION99.07

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