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- PDB-9mkl: canavanyl-tRNAArg deacylase (CtdA) -

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Basic information

Entry
Database: PDB / ID: 9mkl
Titlecanavanyl-tRNAArg deacylase (CtdA)
ComponentsB3/4 domain-containing protein
KeywordsRNA BINDING PROTEIN / canavanyl-tRNAArg / deacylase
Function / homologyB3/4 domain / B3/B4 tRNA-binding domain / Phenylalanyl-tRNA synthetase-like, B3/B4 / B3/4 domain / phenylalanine-tRNA ligase activity / RNA binding / B3/4 domain-containing protein
Function and homology information
Biological speciesSalmonella enterica (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsPage, R. / Peti, W. / Shirakawa, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Mechanistic and evolutionary insights into a family of aminoacyl-tRNA deacylases that protects against canavanine toxicity.
Authors: Maldonado, J.S. / Sepulveda, S. / Karthikeyan, S. / Shirakawa, K.T. / Merced, I. / Radecki, A.A. / Douglas, J. / Peti, W. / Page, R. / Vargas-Rodriguez, O.
History
DepositionDec 17, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: B3/4 domain-containing protein
B: B3/4 domain-containing protein
C: B3/4 domain-containing protein
D: B3/4 domain-containing protein
E: B3/4 domain-containing protein
F: B3/4 domain-containing protein
G: B3/4 domain-containing protein
H: B3/4 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)200,2058
Polymers200,2058
Non-polymers00
Water33,9401884
1
A: B3/4 domain-containing protein
C: B3/4 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)50,0512
Polymers50,0512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: B3/4 domain-containing protein
D: B3/4 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)50,0512
Polymers50,0512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: B3/4 domain-containing protein
H: B3/4 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)50,0512
Polymers50,0512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: B3/4 domain-containing protein
G: B3/4 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)50,0512
Polymers50,0512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.946, 87.604, 98.290
Angle α, β, γ (deg.)63.566, 82.134, 87.401
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
B3/4 domain-containing protein


Mass: 25025.658 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica (bacteria)
Gene: AIY46_02155, AL463_19150, CQW68_08215, EAW95_11030, FJR52_01090, GCH85_00435
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0W4F7L0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1884 / 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: 2.78 Å3/Da / Density % sol: 55.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2M ammonium citrate dibasic, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER IMUS MICROFOCUS / Wavelength: 1.54 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Jul 22, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.98→21.88 Å / Num. obs: 146681 / % possible obs: 97.6 % / Redundancy: 6.9 % / Biso Wilson estimate: 14.56 Å2 / CC1/2: 0.991 / Net I/σ(I): 7.8
Reflection shellResolution: 1.98→2.01 Å / Num. unique obs: 3868 / CC1/2: 0.48

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→21.88 Å / SU ML: 0.239 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 23.065
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2297 1804 1.35 %
Rwork0.1836 132177 -
obs0.1843 133981 89.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.59 Å2
Refinement stepCycle: LAST / Resolution: 1.98→21.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13814 0 0 1884 15698
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005914173
X-RAY DIFFRACTIONf_angle_d0.80519288
X-RAY DIFFRACTIONf_chiral_restr0.04882139
X-RAY DIFFRACTIONf_plane_restr0.00892534
X-RAY DIFFRACTIONf_dihedral_angle_d14.05595292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.030.3136870.27126184X-RAY DIFFRACTION54.11
2.03-2.090.27791320.2379444X-RAY DIFFRACTION82.98
2.09-2.160.26941140.22239699X-RAY DIFFRACTION85.19
2.16-2.240.25331340.21679901X-RAY DIFFRACTION86.69
2.24-2.330.27421470.210410082X-RAY DIFFRACTION88.4
2.33-2.430.2741230.200710139X-RAY DIFFRACTION88.7
2.43-2.560.27721410.203710377X-RAY DIFFRACTION91.62
2.56-2.720.23951560.199410601X-RAY DIFFRACTION92.8
2.72-2.930.2491430.191510988X-RAY DIFFRACTION96.03
2.93-3.230.23271530.1811022X-RAY DIFFRACTION97.02
3.23-3.690.21831600.162411149X-RAY DIFFRACTION97.85
3.69-4.640.17631560.140311268X-RAY DIFFRACTION98.64
4.64-21.880.17481580.156311323X-RAY DIFFRACTION99.45

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