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- PDB-1pyb: Crystal Structure of Aquifex aeolicus Trbp111: a Structure-Specif... -

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Basic information

Entry
Database: PDB / ID: 1pyb
TitleCrystal Structure of Aquifex aeolicus Trbp111: a Structure-Specific tRNA Binding Protein
ComponentstRNA-binding protein Trbp111
KeywordsRNA BINDING PROTEIN / oligonucleotide / oligosaccharide-binding fold / OB-fold / beta-barrel
Function / homology
Function and homology information


methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / tRNA binding / ATP binding
Similarity search - Function
: / Methionyl-tRNA synthetase, beta subunit, C-terminal / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Methionyl-tRNA synthetase beta subunit
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSwairjo, M.A. / Morales, A.J. / Wang, C.C. / Ortiz, A.R. / Schimmel, P.
Citation
Journal: Embo J. / Year: 2000
Title: Crystal structure of trbp111: a structure-specific tRNA-binding protein.
Authors: Swairjo, M.A. / Morales, A.J. / Wang, C.C. / Ortiz, A.R. / Schimmel, P.
#1: Journal: Embo J. / Year: 1999
Title: Structure-Specific tRNA-Binding Protein From the Extreme Thermophile Aquifex aeolicus
Authors: Morales, A.J. / Swairjo, M.A. / Schimmel, P.
History
DepositionJul 8, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4May 1, 2019Group: Data collection / Structure summary / Category: entity / struct_biol / Item: _entity.pdbx_description
Revision 1.5Sep 2, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.6Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA-binding protein Trbp111
B: tRNA-binding protein Trbp111
C: tRNA-binding protein Trbp111
D: tRNA-binding protein Trbp111


Theoretical massNumber of molelcules
Total (without water)48,4494
Polymers48,4494
Non-polymers00
Water3,135174
1
A: tRNA-binding protein Trbp111
B: tRNA-binding protein Trbp111


Theoretical massNumber of molelcules
Total (without water)24,2242
Polymers24,2242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-14 kcal/mol
Surface area12350 Å2
MethodPISA
2
C: tRNA-binding protein Trbp111
D: tRNA-binding protein Trbp111


Theoretical massNumber of molelcules
Total (without water)24,2242
Polymers24,2242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-12 kcal/mol
Surface area12100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.400, 72.790, 68.940
Angle α, β, γ (deg.)90.00, 91.93, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological unit is the homodimer. There are two homodimers in the asymmetric unit. dimer1: chains A & B, dimer2: chains C & D

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Components

#1: Protein
tRNA-binding protein Trbp111


Mass: 12112.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: metG / Plasmid: pTSMg32 / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: O66738
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 3.76 Å3/Da / Density % sol: 67.3 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: PEG2000, ammonium sulfate, imidazole, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 290.15K
Crystal grow
*PLUS
Temperature: 17 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130 %PEG20001drop
20.24 Mammonium sulfate1drop
30.1 Mimidazole1droppH7.2
424 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 3, 1999
RadiationMonochromator: cylidrically bent single crystals Si(111) with horizontal focus
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 26611 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.05 / Rsym value: 0.042 / Net I/σ(I): 9.7
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1244 / Rsym value: 0.361 / % possible all: 88.4
Reflection
*PLUS
Highest resolution: 2.4 Å / Rmerge(I) obs: 0.042
Reflection shell
*PLUS
% possible obs: 88.4 % / Rmerge(I) obs: 0.361

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PXF

1pxf
PDB Unreleased entry


Resolution: 2.5→20 Å / Isotropic thermal model: overall, then group / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1173 -random
Rwork0.208 ---
all0.209 23144 --
obs0.226 23144 84 %-
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3256 0 0 174 3430
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.6
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
2.5-2.610.2281300.246X-RAY DIFFRACTION259496
2.61-2.750.24321280.246X-RAY DIFFRACTION269996
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
Refinement
*PLUS
Lowest resolution: 20 Å / Num. reflection obs: 23601 / % reflection Rfree: 10 % / Rfactor Rfree: 0.22 / Rfactor Rwork: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS

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