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- PDB-8ofe: E.coli Peptide Deformylase with bound inhibitor -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8ofe
TitleE.coli Peptide Deformylase with bound inhibitor
ComponentsPeptide deformylase
KeywordsHYDROLASE / Peptide Deformylase (EC 3.5.1.88) / Inhibitor
Function / homology
Function and homology information


co-translational protein modification / peptide deformylase / peptide deformylase activity / translation / metal ion binding
Similarity search - Function
Peptide deformylase / Peptide deformylase superfamily / Polypeptide deformylase
Similarity search - Domain/homology
Chem-VLK / Peptide deformylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsKirschner, H. / Stoll, R. / Hofmann, E.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research16GW0224 Germany
CitationJournal: Chemmedchem / Year: 2024
Title: Structural Insights into Antibacterial Payload Release from Gold Nanoparticles Bound to E. coli Peptide Deformylase.
Authors: Kirschner, H. / John, M. / Zhou, T. / Bachmann, N. / Schultz, A. / Hofmann, E. / Bandow, J.E. / Scherkenbeck, J. / Metzler-Nolte, N. / Stoll, R.
History
DepositionMar 15, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Apr 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0203
Polymers19,5531
Non-polymers4672
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8790 Å2
Unit cell
Length a, b, c (Å)54.620, 54.620, 231.730
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein Peptide deformylase


Mass: 19552.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: def / Production host: Escherichia coli (E. coli) / References: UniProt: C3SRA2
#2: Chemical ChemComp-VLK / (2R)-2-[[methanoyl(oxidanyl)amino]methyl]-N-[(2S)-3-methyl-1-oxidanylidene-1-[2-(sulfanylmethyl)pyrrolidin-1-yl]butan-2-yl]heptanamide


Mass: 401.564 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H35N3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.17M Ammonium sulfate, 15% Glycerol, 25.5% PEG4000, 50mM Hepes pH7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.91978 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91978 Å / Relative weight: 1
ReflectionResolution: 1.4→47.3 Å / Num. obs: 76134 / % possible obs: 100 % / Redundancy: 63.462 % / Biso Wilson estimate: 29.895 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.113 / Rrim(I) all: 0.114 / Net I/σ(I): 20.75
Reflection shellResolution: 1.4→1.44 Å / Redundancy: 62.6145 % / Rmerge(I) obs: 3.83 / Mean I/σ(I) obs: 0.59 / Num. unique obs: 5626 / CC1/2: 0.61 / Rrim(I) all: 3.86 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSVERSION Jan 10, 2022 BUILT=20220120data reduction
XSCALEVERSION Jan 10, 2022 BUILT=20220120data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→43.79 Å / SU ML: 0.1847 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.9594
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2042 3794 5.01 %
Rwork0.1713 71872 -
obs0.1729 75666 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.04 Å2
Refinement stepCycle: LAST / Resolution: 1.4→43.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1315 0 22 113 1450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01281377
X-RAY DIFFRACTIONf_angle_d1.19071857
X-RAY DIFFRACTIONf_chiral_restr0.0852214
X-RAY DIFFRACTIONf_plane_restr0.0093247
X-RAY DIFFRACTIONf_dihedral_angle_d15.5362557
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.59091160.47672262X-RAY DIFFRACTION85.66
1.42-1.440.40311380.33542666X-RAY DIFFRACTION97.97
1.44-1.460.33441370.25792643X-RAY DIFFRACTION99.68
1.46-1.480.27511480.23452741X-RAY DIFFRACTION99.86
1.48-1.50.25591380.2242633X-RAY DIFFRACTION99.82
1.5-1.520.22861490.22072686X-RAY DIFFRACTION99.79
1.52-1.550.22131400.21382600X-RAY DIFFRACTION99.93
1.55-1.570.27951430.21912750X-RAY DIFFRACTION99.9
1.57-1.60.29361470.19232698X-RAY DIFFRACTION99.93
1.6-1.630.22781400.18632615X-RAY DIFFRACTION99.96
1.63-1.670.22391430.17012695X-RAY DIFFRACTION100
1.67-1.70.20141420.16282693X-RAY DIFFRACTION100
1.7-1.740.191380.15812643X-RAY DIFFRACTION99.89
1.74-1.790.21061390.15032690X-RAY DIFFRACTION100
1.79-1.830.23481410.14982692X-RAY DIFFRACTION99.96
1.83-1.890.21511380.14482705X-RAY DIFFRACTION100
1.89-1.950.20121430.15692696X-RAY DIFFRACTION100
1.95-2.020.17391370.14772662X-RAY DIFFRACTION100
2.02-2.10.17791430.14112706X-RAY DIFFRACTION100
2.1-2.20.15521400.13172639X-RAY DIFFRACTION100
2.2-2.310.18351430.1452670X-RAY DIFFRACTION100
2.31-2.460.19581470.14592696X-RAY DIFFRACTION100
2.46-2.650.18431380.16582658X-RAY DIFFRACTION100
2.65-2.910.21661430.17262686X-RAY DIFFRACTION100
2.91-3.330.1871390.17512666X-RAY DIFFRACTION100
3.33-4.20.22151460.1692715X-RAY DIFFRACTION100
4.2-43.790.19441380.19432666X-RAY DIFFRACTION99.75

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