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- PDB-9iuw: Structure of AlaX-M trans-editing enzyme from Pyrococcus furiosus -

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Basic information

Entry
Database: PDB / ID: 9iuw
TitleStructure of AlaX-M trans-editing enzyme from Pyrococcus furiosus
ComponentsPartial alanyl-tRNA synthetase matches COOH terminus
KeywordsMETAL BINDING PROTEIN / Esterase / aminoacyl-tRNA hydrolase
Function / homology
Function and homology information


alanine-tRNA ligase activity / alanyl-tRNA aminoacylation / aminoacyl-tRNA deacylase activity / nucleic acid binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
: / Alanyl-tRNA synthetase, class IIc, N-terminal / Alanyl-tRNA synthetase, class IIc, core domain / tRNA synthetases class II (A) / Alanyl-transfer RNA synthetases family profile. / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / Translation protein, beta-barrel domain superfamily
Similarity search - Domain/homology
Partial alanyl-tRNA synthetase matches COOH terminus
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsPawar, K.I. / Gogoi, J. / Sankaranarayanan, R.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR)MLP-0162 India
CitationJournal: To Be Published
Title: Structure of AlaX-M trans-editing enzyme from Pyrococcus furiosus
Authors: Pawar, K.I. / Gogoi, J. / Sankaranarayanan, R.
History
DepositionJul 22, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Partial alanyl-tRNA synthetase matches COOH terminus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2263
Polymers25,0961
Non-polymers1312
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-35 kcal/mol
Surface area9700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.230, 37.080, 59.070
Angle α, β, γ (deg.)90.00, 103.56, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-487-

HOH

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Components

#1: Protein Partial alanyl-tRNA synthetase matches COOH terminus / AlaX-M


Mass: 25095.623 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea)
Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF0086 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U4J9
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.4 Å3/Da / Density % sol: 48.79 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Sodium acetate trihydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 30% w/v Polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 27, 2011 / Details: VariMax HF optic
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.78→35.77 Å / Num. obs: 23027 / % possible obs: 99.26 % / Redundancy: 2.4 % / Biso Wilson estimate: 16.06 Å2 / CC1/2: 0.99 / CC star: 0.99 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.06 / Net I/σ(I): 11.78
Reflection shellResolution: 1.78→1.84 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 3.88 / Num. unique obs: 5127 / CC1/2: 0.93 / CC star: 0.98 / Rrim(I) all: 0.23 / % possible all: 99.04

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→35.77 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2166 3333 8.58 %Random selection
Rwork0.1889 ---
obs0.1913 23026 86.05 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.87 Å2
Refinement stepCycle: LAST / Resolution: 1.78→35.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1655 0 2 103 1760
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071694
X-RAY DIFFRACTIONf_angle_d0.8682303
X-RAY DIFFRACTIONf_dihedral_angle_d6.072232
X-RAY DIFFRACTIONf_chiral_restr0.056249
X-RAY DIFFRACTIONf_plane_restr0.009295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.80.25081330.20781327X-RAY DIFFRACTION78
1.8-1.830.21491360.18751408X-RAY DIFFRACTION83
1.83-1.860.26771360.20061456X-RAY DIFFRACTION83
1.86-1.890.24961360.20221430X-RAY DIFFRACTION85
1.89-1.920.25011300.20591393X-RAY DIFFRACTION83
1.92-1.950.21521340.20111484X-RAY DIFFRACTION84
1.95-1.990.25631360.19391461X-RAY DIFFRACTION85
1.99-2.030.28441360.18781429X-RAY DIFFRACTION84
2.03-2.080.23131370.18921457X-RAY DIFFRACTION85
2.08-2.120.24191440.1871465X-RAY DIFFRACTION85
2.12-2.180.21281390.19141491X-RAY DIFFRACTION85
2.18-2.240.21691340.18891445X-RAY DIFFRACTION87
2.24-2.30.2181350.1841501X-RAY DIFFRACTION86
2.3-2.380.22741440.19261509X-RAY DIFFRACTION87
2.38-2.460.21791380.19411509X-RAY DIFFRACTION87
2.46-2.560.2461390.20191479X-RAY DIFFRACTION88
2.56-2.680.2161400.20571524X-RAY DIFFRACTION87
2.68-2.820.26581460.20981497X-RAY DIFFRACTION88
2.82-2.990.22521450.2131511X-RAY DIFFRACTION88
2.99-3.220.23871410.21351537X-RAY DIFFRACTION89
3.22-3.550.21431390.19111540X-RAY DIFFRACTION89
3.55-4.060.16681460.16351538X-RAY DIFFRACTION89
4.06-5.110.17471380.14851542X-RAY DIFFRACTION90
5.12-35.770.17831510.17871573X-RAY DIFFRACTION91

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