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- PDB-4eox: X-ray Structure of Polypeptide Deformylase Bound to a Acylprolina... -

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Basic information

Entry
Database: PDB / ID: 4eox
TitleX-ray Structure of Polypeptide Deformylase Bound to a Acylprolinamide inhibitor
ComponentsPeptide deformylase
Keywordshydrolase/hydrolase inhibitor / Alpha-beta / peptide deformylase metal ion binding / 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-0S5 / NICKEL (II) ION / Peptide deformylase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.783 Å
AuthorsWard, P. / Campobasso, N.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2012
Title: Acylprolinamides: a new class of peptide deformylase inhibitors with in vivo antibacterial activity.
Authors: Axten, J.M. / Medina, J.R. / Blackledge, C.W. / Duquenne, C. / Grant, S.W. / Bobko, M.A. / Peng, T. / Miller, W.H. / Pinckney, T. / Gallagher, T.F. / Kulkarni, S. / Lewandowski, T. / Van ...Authors: Axten, J.M. / Medina, J.R. / Blackledge, C.W. / Duquenne, C. / Grant, S.W. / Bobko, M.A. / Peng, T. / Miller, W.H. / Pinckney, T. / Gallagher, T.F. / Kulkarni, S. / Lewandowski, T. / Van Aller, G.S. / Zonis, R. / Ward, P. / Campobasso, N.
History
DepositionApr 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)23,1953
Polymers22,7211
Non-polymers4742
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.681, 49.681, 92.748
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Peptide deformylase / PDF / Polypeptide deformylase


Mass: 22721.049 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: ATCC BAA-255 / R6 / Gene: def, spr1310 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DP79, 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-0S5 / N-benzoyl-1-[(2R)-3-cyclopentyl-2-{[formyl(hydroxy)amino]methyl}propanoyl]-L-prolinamide


Mass: 415.483 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H29N3O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.52 Å3/Da / Density % sol: 51.17 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, 2 M Ammonium Sulfate, 2% PEG400, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 4, 2009
RadiationMonochromator: diamond laue monochromators from JJ x-ray / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.78→92.75 Å / Num. all: 21455 / Num. obs: 21449 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 17.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIXmodel building
PHENIX(phenix.refine: dev_934)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.783→49.681 Å / SU ML: 0.19 / σ(F): 1.35 / Phase error: 22.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2296 1092 5.1 %random
Rwork0.182 ---
obs0.1845 21400 99.86 %-
all-21437 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.442 Å2 / ksol: 0.356 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.8799 Å2-0 Å20 Å2
2--4.8799 Å20 Å2
3----9.7597 Å2
Refinement stepCycle: LAST / Resolution: 1.783→49.681 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1504 0 31 153 1688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191561
X-RAY DIFFRACTIONf_angle_d1.7452107
X-RAY DIFFRACTIONf_dihedral_angle_d14.82593
X-RAY DIFFRACTIONf_chiral_restr0.132238
X-RAY DIFFRACTIONf_plane_restr0.011277
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7832-1.86440.28991270.22932513X-RAY DIFFRACTION100
1.8644-1.96270.25291470.19112532X-RAY DIFFRACTION100
1.9627-2.08570.22251250.18412538X-RAY DIFFRACTION100
2.0857-2.24670.22771480.18012543X-RAY DIFFRACTION100
2.2467-2.47280.25531430.18252526X-RAY DIFFRACTION100
2.4728-2.83060.25621300.19312540X-RAY DIFFRACTION100
2.8306-3.56610.22031450.1882539X-RAY DIFFRACTION100
3.5661-49.70030.20311270.16422577X-RAY DIFFRACTION100

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