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- PDB-6ow7: X-ray Structure of Polypeptide Deformylase with a Piperazic Acid -

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Basic information

Entry
Database: PDB / ID: 6ow7
TitleX-ray Structure of Polypeptide Deformylase with a Piperazic Acid
ComponentsPeptide deformylase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Inhibitor / complex / metal protein / enzyme / HYDROLASE-HYDROLASE INHIBITOR complex
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 / Peptide deformylase / Peptide deformylase superfamily / Polypeptide deformylase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-N9Y / NICKEL (II) ION / Peptide deformylase / Peptide deformylase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
P: Peptide deformylase
Q: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2968
Polymers45,1802
Non-polymers1,1166
Water3,801211
1
P: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1484
Polymers22,5901
Non-polymers5583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
Q: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1484
Polymers22,5901
Non-polymers5583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.229, 69.229, 91.879
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

#1: Protein Peptide deformylase / PDF / Polypeptide deformylase


Mass: 22589.854 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-N9Y / (3S)-2-{(2R)-2-(cyclopentylmethyl)-3-[formyl(hydroxy)amino]propanoyl}-N-(pyridin-2-yl)hexahydropyridazine-3-carboxamide


Mass: 403.475 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H29N5O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.55 Å3/Da / Density % sol: 51.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1 % - 4 % PEG400 45 % - 55% Ammonium Sulfate 0.1 M HEPES

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→38.28 Å / Num. obs: 72134 / % possible obs: 94 % / Redundancy: 3.6 % / Biso Wilson estimate: 20.58 Å2 / Net I/σ(I): 42.6
Reflection shellResolution: 1.45→1.5 Å / Num. unique obs: 5088 / % possible all: 66.6

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→38.28 Å / SU ML: 0.1674 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.9858
RfactorNum. reflection% reflection
Rfree0.2179 1992 2.76 %
Rwork0.2059 --
obs0.2063 72063 94.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.45 Å2
Refinement stepCycle: LAST / Resolution: 1.45→38.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3031 0 70 211 3312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00583150
X-RAY DIFFRACTIONf_angle_d0.80854253
X-RAY DIFFRACTIONf_chiral_restr0.0783480
X-RAY DIFFRACTIONf_plane_restr0.0047552
X-RAY DIFFRACTIONf_dihedral_angle_d11.59431191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.490.298870.26973310X-RAY DIFFRACTION62.47
1.49-1.530.24551140.25134188X-RAY DIFFRACTION79.34
1.53-1.570.24241410.23494749X-RAY DIFFRACTION89.15
1.57-1.620.23741400.21865008X-RAY DIFFRACTION94.7
1.62-1.680.25081500.21565213X-RAY DIFFRACTION98.53
1.68-1.750.23171560.21455279X-RAY DIFFRACTION99.93
1.75-1.830.28291480.21935297X-RAY DIFFRACTION99.98
1.83-1.920.24091520.22455309X-RAY DIFFRACTION99.95
1.92-2.040.22611490.21455304X-RAY DIFFRACTION99.95
2.04-2.20.23771520.20555292X-RAY DIFFRACTION99.96
2.2-2.420.23781500.21125293X-RAY DIFFRACTION99.94
2.42-2.770.22461530.21555337X-RAY DIFFRACTION99.93
2.77-3.50.20631530.21075315X-RAY DIFFRACTION99.82
3.5-38.290.18751470.18095177X-RAY DIFFRACTION95.93

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