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- PDB-3sw8: Strep Peptide Deformylase with a time dependent dichlorobenzamide... -

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Basic information

Entry
Database: PDB / ID: 3sw8
TitleStrep Peptide Deformylase with a time dependent dichlorobenzamide-reverse hydroxamic acid
ComponentsPeptide deformylase 3
KeywordsHYDROLASE/HYDROLASE INHIBITOR / alpha-beta / peptide deformylase / metal binding protein / 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-5LI / NICKEL (II) ION / Peptide deformylase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.702 Å
AuthorsCampobasso, N. / Smith, K.J.
Citation
Journal: Biochemistry / Year: 2011
Title: Understanding the origins of time-dependent inhibition by polypeptide deformylase inhibitors.
Authors: Totoritis, R. / Duraiswami, C. / Taylor, A.N. / Kerrigan, J.J. / Campobasso, N. / Smith, K.J. / Ward, P. / King, B.W. / Murrayz-Thompson, M. / Jones, A.D. / Van Aller, G.S. / Aubart, K.M. / ...Authors: Totoritis, R. / Duraiswami, C. / Taylor, A.N. / Kerrigan, J.J. / Campobasso, N. / Smith, K.J. / Ward, P. / King, B.W. / Murrayz-Thompson, M. / Jones, A.D. / Van Aller, G.S. / Aubart, K.M. / Zalacain, M. / Thrall, S.H. / Meek, T.D. / Schwartz, B.
#1: Journal: Protein Sci. / Year: 2003
Title: Structural variation and inhibitor binding in polypeptide deformylase from four different bacterial species.
Authors: Smith, K.J. / Petit, C.M. / Aubart, K. / Smyth, M. / McManus, E. / Jones, J. / Fosberry, A. / Lewis, C. / Lonetto, M. / Christensen, S.B.
History
DepositionJul 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2011Group: Database references
Revision 1.2Apr 16, 2014Group: Other
Revision 1.3Feb 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

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Assembly

Deposited unit
P: Peptide deformylase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3456
Polymers22,7211
Non-polymers6245
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.015, 50.015, 91.605
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 3 / / PDF 3 / Polypeptide deformylase 3


Mass: 22721.049 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: defB, def3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q939R9, peptide deformylase
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-5LI / 2,3-dichloro-N-{2-[formyl(hydroxy)amino]ethyl}benzamide


Mass: 277.104 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10Cl2N2O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 1.8 - 2.8 M ammonium sulfate, 1 % - 3 % PEG400, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2
DetectorDetector: CCD / Date: Jan 26, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.7→25 Å / Num. obs: 24582 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.702→24.125 Å / SU ML: 0.23 / σ(F): 0 / Phase error: 22.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2226 1940 8.11 %
Rwork0.1931 --
obs0.1955 23920 97.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.761 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.1931 Å20 Å2-0 Å2
2--3.1931 Å2-0 Å2
3----6.3862 Å2
Refinement stepCycle: LAST / Resolution: 1.702→24.125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1523 0 33 168 1724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061576
X-RAY DIFFRACTIONf_angle_d1.042128
X-RAY DIFFRACTIONf_dihedral_angle_d13.026591
X-RAY DIFFRACTIONf_chiral_restr0.072238
X-RAY DIFFRACTIONf_plane_restr0.005279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.702-1.74470.28261230.24691414X-RAY DIFFRACTION89
1.7447-1.79190.22451320.22481520X-RAY DIFFRACTION93
1.7919-1.84460.25591350.20591510X-RAY DIFFRACTION95
1.8446-1.90410.23531320.19341548X-RAY DIFFRACTION95
1.9041-1.97210.25671400.20261547X-RAY DIFFRACTION97
1.9721-2.05110.26081370.19881580X-RAY DIFFRACTION98
2.0511-2.14440.23341400.19471610X-RAY DIFFRACTION99
2.1444-2.25730.25961450.19311593X-RAY DIFFRACTION98
2.2573-2.39860.25771340.19281579X-RAY DIFFRACTION98
2.3986-2.58360.23411390.19111604X-RAY DIFFRACTION99
2.5836-2.84330.21391470.20831602X-RAY DIFFRACTION100
2.8433-3.25390.20511420.1961618X-RAY DIFFRACTION100
3.2539-4.09630.19191470.17671611X-RAY DIFFRACTION99
4.0963-24.12710.20711470.1841644X-RAY DIFFRACTION99

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