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- PDB-1xty: Crystal structure of Sulfolobus solfataricus peptidyl-tRNA hydrolase -

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Basic information

Entry
Database: PDB / ID: 1xty
TitleCrystal structure of Sulfolobus solfataricus peptidyl-tRNA hydrolase
ComponentsPeptidyl-tRNA hydrolase
KeywordsHYDROLASE / mixed beta sheet
Function / homology
Function and homology information


peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / translation / cytosol
Similarity search - Function
Peptidyl-tRNA hydrolase, archaea / Peptidyl-tRNA hydrolase, PTH2 / Peptidyl-tRNA hydrolase PTH2 / Bit1 / Bit1 / Peptidyl-tRNA hydrolase II domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.8 Å
AuthorsFromant, M. / Schmitt, E. / Mechulam, Y. / Lazennec, C. / Plateau, P. / Blanquet, S.
CitationJournal: Biochemistry / Year: 2005
Title: Crystal structure at 1.8 A resolution and identification of active site residues of Sulfolobus solfataricus peptidyl-tRNA hydrolase.
Authors: Fromant, M. / Schmitt, E. / Mechulam, Y. / Lazennec, C. / Plateau, P. / Blanquet, S.
History
DepositionOct 25, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2013Group: Structure summary
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Peptidyl-tRNA hydrolase
B: Peptidyl-tRNA hydrolase
C: Peptidyl-tRNA hydrolase
D: Peptidyl-tRNA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,39012
Polymers52,6224
Non-polymers7698
Water8,971498
1
A: Peptidyl-tRNA hydrolase
B: Peptidyl-tRNA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6956
Polymers26,3112
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-73 kcal/mol
Surface area11360 Å2
MethodPISA
2
C: Peptidyl-tRNA hydrolase
D: Peptidyl-tRNA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6956
Polymers26,3112
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-72 kcal/mol
Surface area11340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.816, 67.232, 85.352
Angle α, β, γ (deg.)90.00, 95.08, 90.00
Int Tables number4
Space group name H-MP1211
Detailschain A and B form a dimer chain C and D form dimer

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Components

#1: Protein
Peptidyl-tRNA hydrolase / PTH


Mass: 13155.490 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: DSM1617 / Gene: pth / Plasmid: pET-pthS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-rosetta / References: UniProt: Q980V1, peptidyl-tRNA hydrolase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / 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: 2.5 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 297 K / Method: vapor diffusion / pH: 2.8
Details: 0.8Ml SO4, 1.6% PEG 8000, pH 2.8, VAPOR DIFFUSION, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.999 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 15, 2003
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 48937 / Num. obs: 48937 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 18.6 Å2 / Rsym value: 0.065
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 3.8 % / Num. unique all: 3544 / Rsym value: 0.112 / % possible all: 99.5

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.8→46.6 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.224 2925 RANDOM
Rwork0.205 --
obs0.205 48488 -
all-48488 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.589 Å20 Å2-1.351 Å2
2--1.582 Å20 Å2
3----4.171 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3680 0 40 498 4218
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004984
X-RAY DIFFRACTIONc_angle_deg1.12346
LS refinement shellResolution: 1.8→1.81 Å
RfactorNum. reflection
Rfree0.3009 60
Rwork0.2546 -
obs-876

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