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- PDB-4djj: Crystal structure of the complex of Peptidyl-tRNA hydrolase from ... -

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Basic information

Entry
Database: PDB / ID: 4djj
TitleCrystal structure of the complex of Peptidyl-tRNA hydrolase from Pseudomonas aeruginosa with Pimelic acid at 2.9 Angstrom resolution
ComponentsPeptidyl-tRNA hydrolaseAlternative ribosome-rescue factor B
KeywordsHYDROLASE / esterase
Function / homology
Function and homology information


peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / translation / 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
PIMELIC ACID / Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.94 Å
AuthorsKumar, A. / Singh, A. / Singh, N. / Sinha, M. / Sharma, S. / Arora, A. / Singh, T.P.
CitationJournal: To be Published
Title: Crystal structure of the complex of Peptidyl-tRNA hydrolase from Pseudomonas aeruginosa with Pimelic acid at 2.9 Angstrom resolution
Authors: Kumar, A. / Singh, A. / Singh, N. / Sinha, M. / Sharma, S. / Arora, A. / Singh, T.P.
History
DepositionFeb 2, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: Peptidyl-tRNA hydrolase
B: Peptidyl-tRNA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9864
Polymers41,6662
Non-polymers3202
Water2,000111
1
A: Peptidyl-tRNA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9932
Polymers20,8331
Non-polymers1601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptidyl-tRNA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9932
Polymers20,8331
Non-polymers1601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.024, 65.024, 160.163
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Peptidyl-tRNA hydrolase / Alternative ribosome-rescue factor B / PTH


Mass: 20832.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA4672, pth / Plasmid: pET-NH6 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3) / References: UniProt: Q9HVC3, peptidyl-tRNA hydrolase
#2: Chemical ChemComp-PML / PIMELIC ACID / Pimelic acid


Mass: 160.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H12O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M HEPES pH 8.5, PEG 4000, 5% Isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.514 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2012 / Details: Mirror
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.514 Å / Relative weight: 1
ReflectionResolution: 2.94→56.3 Å / Num. obs: 8159 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 53.7 Å2 / Rsym value: 0.147 / Net I/σ(I): 8.1
Reflection shellResolution: 2.94→3.05 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.393 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3P2J

3p2j


Resolution: 2.94→56.3 Å / Occupancy max: 1 / Occupancy min: 0.8 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2181 442 5.4 %Random
Rwork0.204 ---
obs-8147 --
Solvent computationBsol: 49.643 Å2
Displacement parametersBiso max: 74.21 Å2 / Biso mean: 38.4112 Å2 / Biso min: 5.19 Å2
Baniso -1Baniso -2Baniso -3
1--1.049 Å2-8.849 Å20 Å2
2---1.049 Å20 Å2
3---2.098 Å2
Refinement stepCycle: LAST / Resolution: 2.94→56.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2934 0 22 111 3067
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it0.9051.5
X-RAY DIFFRACTIONc_scbond_it2.6142
X-RAY DIFFRACTIONc_mcangle_it1.5812
X-RAY DIFFRACTIONc_scangle_it3.8422.5
LS refinement shellResolution: 2.94→3.04 Å
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4carbohydrate.param
X-RAY DIFFRACTION5pml.param

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