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- PDB-4xkz: Crystal structure of the C-terminal anticodon loop binding domain... -

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Basic information

Entry
Database: PDB / ID: 4xkz
TitleCrystal structure of the C-terminal anticodon loop binding domain of a valyl-tRNA synthetase from Pseudomonas aeruginosa
ComponentsValine-tRNA ligase
KeywordsLIGASE / structural genomics / aminoacylation / tRNA binding / protein synthesis / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


valine-tRNA ligase / valine-tRNA ligase activity / valyl-tRNA aminoacylation / tRNA aminoacylation for protein translation / aminoacyl-tRNA editing activity / ATP binding / cytosol
Similarity search - Function
Valine-tRNA ligase / Valyl-tRNA synthetase, tRNA-binding arm / Valyl tRNA synthetase, anticodon-binding domain / Valyl tRNA synthetase tRNA binding arm / Valyl-tRNA synthetase, tRNA-binding arm superfamily / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding ...Valine-tRNA ligase / Valyl-tRNA synthetase, tRNA-binding arm / Valyl tRNA synthetase, anticodon-binding domain / Valyl tRNA synthetase tRNA binding arm / Valyl-tRNA synthetase, tRNA-binding arm superfamily / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding / Anticodon-binding domain of tRNA ligase / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
IODIDE ION / TRIETHYLENE GLYCOL / Valine--tRNA ligase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of the C-terminal anticodon loop binding domain of a valyl-tRNA synthetase from Pseudomonas aeruginosa.
Authors: Edwards, T.E. / Fox III, D. / Manoil, C.
History
DepositionJan 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_assembly ...entity_src_gen / pdbx_struct_assembly / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Valine-tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5377
Polymers30,7291
Non-polymers8086
Water4,936274
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.360, 103.360, 79.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein Valine-tRNA ligase / Valyl-tRNA synthetase / ValRS


Mass: 30729.281 Da / Num. of mol.: 1
Fragment: C-terminal anticodon loop binding domain (UNP residues 639-898)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: valS, PA3834 / Plasmid: BG1861 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HXH0, valine-tRNA ligase
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 3.44 Å3/Da / Density % sol: 64.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PsaeA.18849.a.B4.PW37589 at 18 mg/mL against Morpheus screen condition B6 10% PEG 8000, 20% ethylene glycol, 0.1 M MOPS-HEPES, pH7.5, 0.03 M sodium fluoride, 0.03 M sodium bromide, 0.03 M ...Details: PsaeA.18849.a.B4.PW37589 at 18 mg/mL against Morpheus screen condition B6 10% PEG 8000, 20% ethylene glycol, 0.1 M MOPS-HEPES, pH7.5, 0.03 M sodium fluoride, 0.03 M sodium bromide, 0.03 M sodium iodide, crystal tracking ID 259627b6, unique puck ID oaf3-9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 31655 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 31.84 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.068 / Χ2: 0.953 / Net I/σ(I): 20.8 / Num. measured all: 236363
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.95-20.9390.4693.7517404230923090.503100
2-2.060.960.3694.8116879224722430.39699.8
2.06-2.120.9750.2856.2616475218921870.30699.9
2.12-2.180.9820.2387.4616132214321420.256100
2.18-2.250.9880.1949.0215655208420820.20899.9
2.25-2.330.9910.16610.515150201320070.17899.7
2.33-2.420.9930.13313.0214576193419310.14299.8
2.42-2.520.9960.11414.5614037186618630.12399.8
2.52-2.630.9970.09318.0813464179617910.09999.7
2.63-2.760.9970.07621.9412899172017070.08299.2
2.76-2.910.9980.06724.3612370165116440.07299.6
2.91-3.080.9980.05728.7611553155315410.06199.2
3.08-3.30.9990.04933.4610913147514630.05399.2
3.3-3.560.9990.04140.610145137313640.04499.3
3.56-3.90.9990.03745.489292126812490.03998.5
3.9-4.360.9990.03348.478490117411550.03598.4
4.36-5.040.9990.03250.847422103710140.03597.8
5.04-6.170.9990.03447.3862568938730.03797.8
6.17-8.720.9990.0347.3248197146930.03397.1
8.720.9990.02850.9124324393970.0390.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
XDSdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.1842 / WRfactor Rwork: 0.1497 / FOM work R set: 0.8785 / SU B: 5.475 / SU ML: 0.069 / SU R Cruickshank DPI: 0.1023 / SU Rfree: 0.1059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1934 1585 5 %RANDOM
Rwork0.1558 30043 --
obs0.1576 31655 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.54 Å2 / Biso mean: 35.286 Å2 / Biso min: 17.06 Å2
Baniso -1Baniso -2Baniso -3
1--1.81 Å20 Å20 Å2
2---1.81 Å20 Å2
3---3.62 Å2
Refinement stepCycle: final / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1972 0 24 274 2270
Biso mean--50.36 37.9 -
Num. residues----251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192047
X-RAY DIFFRACTIONr_bond_other_d0.0020.021955
X-RAY DIFFRACTIONr_angle_refined_deg1.7751.952779
X-RAY DIFFRACTIONr_angle_other_deg1.06134474
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2535254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.42123.77698
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01415338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4161518
X-RAY DIFFRACTIONr_chiral_restr0.1150.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212318
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02472
X-RAY DIFFRACTIONr_mcbond_it1.5422.5731007
X-RAY DIFFRACTIONr_mcbond_other1.5372.571006
X-RAY DIFFRACTIONr_mcangle_it2.2923.8441258
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 121 -
Rwork0.214 2182 -
all-2303 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 25.0327 Å / Origin y: 5.8399 Å / Origin z: 15.7221 Å
111213212223313233
T0.0193 Å2-0.0229 Å2-0.005 Å2-0.04 Å2-0.005 Å2--0.0357 Å2
L1.7463 °20.434 °20.1816 °2-0.5991 °20.0747 °2--0.451 °2
S0.0945 Å °-0.2331 Å °0.1199 Å °0.0756 Å °-0.078 Å °-0.01 Å °-0.0299 Å °0.0064 Å °-0.0165 Å °

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