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- PDB-6ow2: X-ray Structure of Polypeptide Deformylase -

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Basic information

Entry
Database: PDB / ID: 6ow2
TitleX-ray Structure of Polypeptide Deformylase
ComponentsPeptide deformylase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Inhibitor / complex / metal protein / enzyme / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


peptide deformylase / peptide deformylase activity / : / translation / metal ion binding
Similarity search - Function
Peptide Deformylase / Peptide deformylase / Peptide deformylase / Peptide deformylase superfamily / Polypeptide deformylase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-NB4 / NICKEL (II) ION / Peptide deformylase / Peptide deformylase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCampobasso, N. / Spletstoser, J. / Ward, P.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2019
Title: Discovery of piperazic acid peptide deformylase inhibitors with in vivo activity for respiratory tract and skin infections.
Authors: Spletstoser, J.T. / Dreabit, J. / Knox, A.N. / Benowitz, A. / Campobasso, N. / Ward, P. / Cui, G. / Lewandowski, T. / McCloskey, L. / Aubart, K.M.
History
DepositionMay 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
P: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1303
Polymers22,5901
Non-polymers5402
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.334, 50.334, 91.482
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw

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Components

#1: Protein Peptide deformylase / PDF / Polypeptide deformylase


Mass: 22589.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria)
Gene: defB, def, def_1, def_2, def_3, A5N45_09745, ERS019420_01538, ERS019688_00954, ERS020178_05158, ERS020534_01685, ERS020726_00048, ERS021057_00383, ERS021733_04069, ERS050646_01998, ERS367886_ ...Gene: defB, def, def_1, def_2, def_3, A5N45_09745, ERS019420_01538, ERS019688_00954, ERS020178_05158, ERS020534_01685, ERS020726_00048, ERS021057_00383, ERS021733_04069, ERS050646_01998, ERS367886_01588, ERS409327_03241, ERS409593_03947, KK0981_34260, NCTC12140_00964
Production host: Escherichia coli (E. coli)
References: UniProt: Q939R9, UniProt: Q8DP79*PLUS, peptide deformylase
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-NB4 / (2R)-2-(cyclopentylmethyl)-N'-{5-fluoro-6-[(9aS)-hexahydropyrazino[2,1-c][1,4]oxazin-8(1H)-yl]-2-methylpyrimidin-4-yl}-3-[hydroxy(hydroxymethyl)amino]propanehydrazide


Mass: 481.564 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H36FN7O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.71 Å3/Da / Density % sol: 54.59 % / Description: rods
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1 % - 4 % PEG400 40% - 56% Ammonium Sulfate 0.1 HEPES

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Data collection

DiffractionMean temperature: 175 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→91 Å / Num. obs: 26688 / % possible obs: 88 % / Redundancy: 4.2 % / Biso Wilson estimate: 19.63 Å2 / Net I/σ(I): 18
Reflection shellResolution: 1.6→1.63 Å / Num. unique obs: 1515

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→33.85 Å / SU ML: 0.2036 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.0664
RfactorNum. reflection% reflection
Rfree0.223 1251 5.07 %
Rwork0.1982 --
obs0.1994 24688 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.2 Å2
Refinement stepCycle: LAST / Resolution: 1.7→33.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1497 0 35 86 1618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00641558
X-RAY DIFFRACTIONf_angle_d0.79572104
X-RAY DIFFRACTIONf_chiral_restr0.056237
X-RAY DIFFRACTIONf_plane_restr0.0046271
X-RAY DIFFRACTIONf_dihedral_angle_d8.9595947
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.770.27591230.24672436X-RAY DIFFRACTION92.05
1.77-1.850.29071540.22832558X-RAY DIFFRACTION98.65
1.85-1.950.26021480.22622605X-RAY DIFFRACTION99.17
1.95-2.070.25721390.20592613X-RAY DIFFRACTION99.64
2.07-2.230.21671300.20282648X-RAY DIFFRACTION99.71
2.23-2.450.24731180.21192642X-RAY DIFFRACTION99.75
2.45-2.810.22481440.21692628X-RAY DIFFRACTION99.96
2.81-3.540.23651530.20172639X-RAY DIFFRACTION99.89
3.54-33.860.1791420.16562668X-RAY DIFFRACTION99.86

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