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- PDB-4l87: Crystal structure of the human seryl-tRNA synthetase in complex w... -

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Basic information

Entry
Database: PDB / ID: 4l87
TitleCrystal structure of the human seryl-tRNA synthetase in complex with Ser-SA at 2.9 Angstrom resolution
ComponentsSerine--tRNA ligase, cytoplasmic
KeywordsLIGASE / long alpha-helices / seven-stranded anti-parallel beta-sheet / aminoacylation / tRNAser
Function / homology
Function and homology information


selenocysteine-tRNA ligase activity / negative regulation of vascular endothelial growth factor production / selenocysteine incorporation / serine-tRNA ligase / serine-tRNA ligase activity / seryl-tRNA aminoacylation / Cytosolic tRNA aminoacylation / tRNA modification / Selenocysteine synthesis / negative regulation of angiogenesis ...selenocysteine-tRNA ligase activity / negative regulation of vascular endothelial growth factor production / selenocysteine incorporation / serine-tRNA ligase / serine-tRNA ligase activity / seryl-tRNA aminoacylation / Cytosolic tRNA aminoacylation / tRNA modification / Selenocysteine synthesis / negative regulation of angiogenesis / cytoplasmic translation / tRNA binding / molecular adaptor activity / translation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of transcription by RNA polymerase II / enzyme binding / protein homodimerization activity / extracellular exosome / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Serine-tRNA synthetase, tRNA binding domain / 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) / Bira Bifunctional Protein; Domain 2 ...Serine-tRNA synthetase, tRNA binding domain / 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) / 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
PHOSPHATE ION / 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE / Serine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.897 Å
AuthorsXu, X. / Yang, X.-L.
CitationJournal: Structure / Year: 2013
Title: Crystal Structure of Human Seryl-tRNA Synthetase and Ser-SA Complex Reveals a Molecular Lever Specific to Higher Eukaryotes.
Authors: Xu, X. / Shi, Y. / Yang, X.L.
History
DepositionJun 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Database references
Revision 1.2Nov 27, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 20, 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 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Serine--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0945
Polymers54,5171
Non-polymers5774
Water0
1
A: Serine--tRNA ligase, cytoplasmic
hetero molecules

A: Serine--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,18810
Polymers109,0352
Non-polymers1,1548
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area8480 Å2
ΔGint-67 kcal/mol
Surface area42070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.074, 167.074, 65.156
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

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Components

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


Mass: 54517.250 Da / Num. of mol.: 1 / Fragment: UNP residues 2-477
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SARS, SERS / Plasmid: PET20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P49591, serine-tRNA ligase
#2: Chemical ChemComp-SSA / 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE


Mass: 433.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H19N7O8S
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 4.82 Å3/Da / Density % sol: 74.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG3350, 0.2 M ammonium fluoride or ammonium formate, 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2012
RadiationMonochromator: Side scattering I-beam bent single crystal, asymmetric cut 4.9650 degrees
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.897→144.69 Å / Num. all: 23528 / Num. obs: 23501 / % possible obs: 95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 9.9 % / Biso Wilson estimate: 65.19 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 6.2
Reflection shellHighest resolution: 2.897 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3VBB

3vbb


Resolution: 2.897→144.69 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.91 / Occupancy max: 1 / Occupancy min: 1 / SU B: 15.825 / SU ML: 0.281 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.565 / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2676 1208 5.1 %RANDOM
Rwork0.2549 ---
obs0.2556 23501 99.89 %-
all-23528 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.28 Å2 / Biso mean: 69.737 Å2 / Biso min: 49.98 Å2
Baniso -1Baniso -2Baniso -3
1-2.71 Å21.36 Å20 Å2
2--2.71 Å20 Å2
3----4.07 Å2
Refinement stepCycle: LAST / Resolution: 2.897→144.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3827 0 36 0 3863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0193937
X-RAY DIFFRACTIONr_angle_refined_deg0.8671.9815312
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9695475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.87424.233189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.31815728
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.3141529
X-RAY DIFFRACTIONr_chiral_restr0.0490.2580
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212954
LS refinement shellResolution: 2.897→2.972 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 74 -
Rwork0.39 1562 -
all-1636 -
obs--99.7 %

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