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- PDB-8axp: Neisseria gonorrhoeae peptidyl-tRNA hydrolase complexed with an X... -

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Basic information

Entry
Database: PDB / ID: 8axp
TitleNeisseria gonorrhoeae peptidyl-tRNA hydrolase complexed with an XChem hit.
ComponentsPeptidyl-tRNA hydrolase
KeywordsHYDROLASE / Inhibitor / Complex
Function / homology
Function and homology information


peptidyl-tRNA hydrolase / peptidyl-tRNA hydrolase activity / translation / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
N-[4-(2-amino-1,3-thiazol-4-yl)phenyl]acetamide / Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsRoe, S.M. / Fearon, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Org.Lett. / Year: 2022
Title: Synthesis of a Thiazole Library via an Iridium-Catalyzed Sulfur Ylide Insertion Reaction.
Authors: Hassell-Hart, S. / Speranzini, E. / Srikwanjai, S. / Hossack, E. / Roe, S.M. / Fearon, D. / Akinbosede, D. / Hare, S. / Spencer, J.
History
DepositionAug 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,09811
Polymers42,9592
Non-polymers1,1399
Water5,260292
1
B: Peptidyl-tRNA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0976
Polymers21,4801
Non-polymers6185
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Peptidyl-tRNA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0015
Polymers21,4801
Non-polymers5214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.440, 71.510, 146.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Peptidyl-tRNA hydrolase / PTH


Mass: 21479.639 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Strain: NCCP11945 / Gene: pth, NGK_0538 / Production host: Escherichia coli (E. coli) / References: UniProt: B4RK78, peptidyl-tRNA hydrolase
#2: Chemical ChemComp-O0J / N-[4-(2-amino-1,3-thiazol-4-yl)phenyl]acetamide


Mass: 233.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H11N3OS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.66 Å3/Da / Density % sol: 53.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.95
Details: 60uL of the reservoir solution (100 mM Bis-Tris Propane pH 5.95, 200 mM Li2SO4 and 30% PEG 3350) was pipetted into the wells. The drop volume was 0.5uL, composed of 200 nL of 13.7 mg/mL ...Details: 60uL of the reservoir solution (100 mM Bis-Tris Propane pH 5.95, 200 mM Li2SO4 and 30% PEG 3350) was pipetted into the wells. The drop volume was 0.5uL, composed of 200 nL of 13.7 mg/mL gonoccocal Pth, 200 nL reservoir solution and 100 nL seed crystals. The plate was sealed quickly and kept in an incubator at 18C and the single crystals appeared in 2-7 days.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.83→37.4 Å / Num. obs: 38126 / % possible obs: 92.2 % / Redundancy: 6.3 % / Biso Wilson estimate: 27.96 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.032 / Rrim(I) all: 0.079 / Net I/σ(I): 16.5
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 6.8 % / Rmerge(I) obs: 2.042 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2032 / CC1/2: 0.669 / Rpim(I) all: 0.841 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5..8.0349refinement
PHENIX1.20_4459refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QT4

4qt4


Resolution: 1.83→37.4 Å / SU ML: 0.3752 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 46.0471
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3641 1916 5.1 %
Rwork0.3345 35667 -
obs0.336 37583 90.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.49 Å2
Refinement stepCycle: LAST / Resolution: 1.83→37.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2965 0 67 292 3324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00563101
X-RAY DIFFRACTIONf_angle_d0.88164195
X-RAY DIFFRACTIONf_chiral_restr0.0527430
X-RAY DIFFRACTIONf_plane_restr0.0071568
X-RAY DIFFRACTIONf_dihedral_angle_d5.7197434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.880.49651560.4122749X-RAY DIFFRACTION99.59
1.88-1.930.49111080.46842148X-RAY DIFFRACTION79.02
1.93-1.980.6173580.54161252X-RAY DIFFRACTION45.41
1.98-2.050.63631170.55412662X-RAY DIFFRACTION95.53
2.05-2.120.46591390.4482724X-RAY DIFFRACTION99.31
2.12-2.210.45651270.46422798X-RAY DIFFRACTION99.52
2.21-2.310.7493950.6011743X-RAY DIFFRACTION62.99
2.31-2.430.60251360.47032657X-RAY DIFFRACTION95.65
2.43-2.580.38151460.37232796X-RAY DIFFRACTION100
2.58-2.780.33591580.35532775X-RAY DIFFRACTION99.76
2.78-3.060.39141650.35572799X-RAY DIFFRACTION99.83
3.06-3.50.34981450.3122822X-RAY DIFFRACTION99.8
3.5-4.410.3041920.2582759X-RAY DIFFRACTION97.33
4.41-37.40.24291740.21052983X-RAY DIFFRACTION99.59

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