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- PDB-8rhr: E.coli Peptide Deformylase with bound inhibitor BB4 -

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Basic information

Entry
Database: PDB / ID: 8rhr
TitleE.coli Peptide Deformylase with bound inhibitor BB4
ComponentsPeptide deformylase
KeywordsHYDROLASE / Peptide Deformylase (EC 3.5.1.88) / Inhibitor
Function / homology
Function and homology information


peptide deformylase / peptide deformylase activity / : / translation / metal ion binding
Similarity search - Function
Peptide deformylase / Peptide deformylase superfamily / Polypeptide deformylase
Similarity search - Domain/homology
2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide / Peptide deformylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.42 Å
AuthorsKirschner, H. / Stoll, R. / Hofmann, E.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research16GW0224 Germany
CitationJournal: J.Med.Chem. / Year: 2024
Title: Toward More Selective Antibiotic Inhibitors: A Structural View of the Complexed Binding Pocket of E. coli Peptide Deformylase.
Authors: Kirschner, H. / Heister, N. / Zouatom, M. / Zhou, T. / Hofmann, E. / Scherkenbeck, J. / Stoll, R.
History
DepositionDec 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: 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

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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)20,1366
Polymers19,5531
Non-polymers5835
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint3 kcal/mol
Surface area9170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.850, 54.850, 228.580
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
Components on special symmetry positions
IDModelComponents
11A-428-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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 / Plasmid: pET19mod
Details (production host): pET19 with additional TEV protease cutting site
Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: C3SRA2

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Non-polymers , 5 types, 136 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BB4 / 2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide


Mass: 269.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H9BrN2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.54 Å3/Da / Density % sol: 51.54 %
Crystal growTemperature: 291.2 K / Method: vapor diffusion, sitting drop
Details: 1 ul of protein solution (10 ug/ul) was mixed with 1 ul reservoir solution (0.17 M ammonium sulfate, 25.5% (w/v) PEG4000, 15% (v/v) glycerol); soaking was performed for appr. 22 hours at 291. ...Details: 1 ul of protein solution (10 ug/ul) was mixed with 1 ul reservoir solution (0.17 M ammonium sulfate, 25.5% (w/v) PEG4000, 15% (v/v) glycerol); soaking was performed for appr. 22 hours at 291.2K with 1 ul of stock solution (30 mM) added to the sitting drop well

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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: 0.91977 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 29, 1022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91977 Å / Relative weight: 1
ReflectionResolution: 1.42→46.51 Å / Num. obs: 72634 / % possible obs: 100 % / Redundancy: 36.9 % / Biso Wilson estimate: 23.89 Å2 / CC1/2: 1 / Rrim(I) all: 0.066 / Rsym value: 0.065 / Net I/σ(I): 27.84
Reflection shellResolution: 1.42→1.46 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 5371 / CC1/2: 0.452 / Rrim(I) all: 3.26 / Rsym value: 3.19 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.42→46.51 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.4611
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1865 3633 5 %
Rwork0.1627 68983 -
obs0.1639 72616 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.58 Å2
Refinement stepCycle: LAST / Resolution: 1.42→46.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1347 0 30 131 1508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01361437
X-RAY DIFFRACTIONf_angle_d1.27361938
X-RAY DIFFRACTIONf_chiral_restr0.0941218
X-RAY DIFFRACTIONf_plane_restr0.0162256
X-RAY DIFFRACTIONf_dihedral_angle_d6.9289197
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.440.34971440.31832690X-RAY DIFFRACTION99.86
1.44-1.460.32781330.28492584X-RAY DIFFRACTION100
1.46-1.480.30211410.24412711X-RAY DIFFRACTION99.93
1.48-1.50.25871370.2312605X-RAY DIFFRACTION99.96
1.5-1.520.25171470.20762696X-RAY DIFFRACTION99.96
1.52-1.550.26411360.18712594X-RAY DIFFRACTION99.96
1.55-1.580.21161430.18152702X-RAY DIFFRACTION100
1.58-1.610.21961400.17282649X-RAY DIFFRACTION100
1.61-1.640.20651370.16662641X-RAY DIFFRACTION99.96
1.64-1.670.20121440.1492678X-RAY DIFFRACTION99.89
1.67-1.710.16161390.14472651X-RAY DIFFRACTION100
1.71-1.750.18541380.14672639X-RAY DIFFRACTION100
1.75-1.790.18281380.13352642X-RAY DIFFRACTION100
1.79-1.840.19521360.13462695X-RAY DIFFRACTION100
1.84-1.890.20461430.1282640X-RAY DIFFRACTION99.96
1.89-1.950.20561410.13682649X-RAY DIFFRACTION99.96
1.95-2.020.17891430.14192659X-RAY DIFFRACTION100
2.02-2.10.16931390.14232641X-RAY DIFFRACTION100
2.1-2.20.15361430.12842663X-RAY DIFFRACTION99.96
2.2-2.310.18091380.132625X-RAY DIFFRACTION99.93
2.31-2.460.17621450.1462649X-RAY DIFFRACTION99.89
2.46-2.650.22481330.16392647X-RAY DIFFRACTION100
2.65-2.920.18061350.16682659X-RAY DIFFRACTION99.86
2.92-3.340.16421350.1662653X-RAY DIFFRACTION99.96
3.34-4.210.21731430.16322671X-RAY DIFFRACTION100
4.21-46.510.15631420.1852650X-RAY DIFFRACTION99.86

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