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- PDB-2pth: PEPTIDYL-TRNA HYDROLASE FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 2pth
TitlePEPTIDYL-TRNA HYDROLASE FROM ESCHERICHIA COLI
ComponentsPEPTIDYL-TRNA HYDROLASE
KeywordsHYDROLASE / PEPTIDYL-TRNA
Function / homology
Function and homology information


peptidyl-tRNA hydrolase / peptidyl-tRNA hydrolase activity / protein quality control for misfolded or incompletely synthesized proteins / rescue of stalled ribosome / tRNA binding / cytoplasm
Similarity search - Function
Peptidyl-tRNA hydrolase / Peptidyl-tRNA hydrolase signature 2. / Peptidyl-tRNA hydrolase signature 1. / Peptidyl-tRNA hydrolase / Peptidyl-tRNA hydrolase, conserved site / Peptidyl-tRNA hydrolase superfamily / Peptidyl-tRNA hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRS / Resolution: 1.2 Å
AuthorsSchmitt, E. / Mechulam, Y. / Fromant, M. / Plateau, P. / Blanquet, S.
CitationJournal: EMBO J. / Year: 1997
Title: Crystal structure at 1.2 A resolution and active site mapping of Escherichia coli peptidyl-tRNA hydrolase.
Authors: Schmitt, E. / Mechulam, Y. / Fromant, M. / Plateau, P. / Blanquet, S.
History
DepositionMar 25, 1997Processing site: BNL
Revision 1.0Mar 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PEPTIDYL-TRNA HYDROLASE


Theoretical massNumber of molelcules
Total (without water)20,9821
Polymers20,9821
Non-polymers00
Water3,261181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.240, 63.590, 62.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PEPTIDYL-TRNA HYDROLASE


Mass: 20982.115 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Cellular location: CYTOPLASM / Gene: PTH / Plasmid: PUC18 / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / References: UniProt: P0A7D1, peptidyl-tRNA hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.24 Å3/Da / Density % sol: 45.05 %
Crystal growpH: 7.5 / Details: 10% PEG6000,12% ISOPROPANOL, 0,1 M TRIS-CL PH7.5
Crystal grow
*PLUS
Temperature: 6 ℃ / Method: vapor diffusion, hanging drop
Details: Schmitt, E., (1997) Proteins.Struct.Funct.Genet., 28, 135.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-12 %PEG60001reservoir
212 %isopropanol1reservoir
30.1 MTris-HCl1reservoir
42 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.994
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.994 Å / Relative weight: 1
ReflectionResolution: 1.2→28 Å / Num. obs: 55575 / % possible obs: 93.9 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 12.7 Å2 / Rsym value: 0.046 / Net I/σ(I): 8.3
Reflection shellResolution: 1.2→1.23 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 4.6 / Rsym value: 0.15 / % possible all: 85.3
Reflection
*PLUS
Rmerge(I) obs: 0.046

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIRS / Resolution: 1.2→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: SOME WATER MOLECULES ARE IN CLOSE CONTACT. THESE MOLECULES SHOULD BE CONSIDERED AS ALTERNATE POSITIONS, NOT PRESENT SIMULTANEOUSLY IN THE ASYMMETRIC UNIT.
RfactorNum. reflection% reflectionSelection details
Rfree0.215 3276 6 %RANDOM
Rwork0.196 ---
obs0.196 53921 90.8 %-
Displacement parametersBiso mean: 17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.15 Å
Luzzati d res low-8 Å
Refinement stepCycle: LAST / Resolution: 1.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1480 0 0 181 1661
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.2
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.31.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2.32
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shellResolution: 1.2→1.25 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.299 369 6.3 %
Rwork0.281 5517 -
obs--80.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.2

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