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- PDB-5jf3: Crystal structure of type 2 PDF from Streptococcus agalactiae in ... -

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Basic information

Entry
Database: PDB / ID: 5jf3
TitleCrystal structure of type 2 PDF from Streptococcus agalactiae in complex with inhibitor AT018
ComponentsPeptide deformylase
KeywordsHYDROLASE / PDF / type 2 / NME / N-terminal methionine excision / Streptococcus agalactiae / inhibitor / AT018
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
ACETATE ION / IMIDAZOLE / Chem-SF5 / Peptide deformylase
Similarity search - Component
Biological speciesStreptococcus agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsFieulaine, S. / Giglione, C. / Meinnel, T.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-MIME 2006 France
CitationJournal: Sci Rep / Year: 2016
Title: A unique peptide deformylase platform to rationally design and challenge novel active compounds.
Authors: Fieulaine, S. / Alves de Sousa, R. / Maigre, L. / Hamiche, K. / Alimi, M. / Bolla, J.M. / Taleb, A. / Denis, A. / Pages, J.M. / Artaud, I. / Meinnel, T. / Giglione, C.
History
DepositionApr 19, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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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)23,97213
Polymers22,8941
Non-polymers1,07812
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-191 kcal/mol
Surface area10580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.070, 65.490, 88.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Peptide deformylase / PDF / Polypeptide deformylase


Mass: 22894.297 Da / Num. of mol.: 1 / Mutation: S2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Gene: def, gbs1883 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2,pLysS / References: UniProt: Q8E378, peptide deformylase

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Non-polymers , 5 types, 275 molecules

#2: Chemical ChemComp-SF5 / methyl 4-({5-[(3R)-1-(hydroxyamino)-1-oxoheptan-3-yl]-1,2,4-oxadiazol-3-yl}methyl)benzoate


Mass: 361.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H23N3O5
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.61 Å3/Da / Density % sol: 52.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 7% PEG-8000, 100mM imidazole pH7.5, 300mM Zn acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 60836 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.79 % / CC1/2: 0.996 / Rsym value: 0.095 / Net I/σ(I): 9.13
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 3.66 % / Rmerge(I) obs: 0.896 / Mean I/σ(I) obs: 1.72 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
FRODOmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AIE

2aie


Resolution: 1.6→44.41 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.772 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.086 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21406 1615 5 %RANDOM
Rwork0.18583 ---
obs0.18723 30677 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2--0.53 Å20 Å2
3----0.66 Å2
Refinement stepCycle: 1 / Resolution: 1.6→44.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1577 0 33 263 1873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221626
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.992196
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3975202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.62572
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.10515289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.318159
X-RAY DIFFRACTIONr_chiral_restr0.0860.2249
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021212
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.2725
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21132
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.2226
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.170.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.228
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1030.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0790.22
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8181.51046
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.321631
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3623637
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7314.5565
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 118 -
Rwork0.317 2235 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -7.415 Å / Origin y: -7.054 Å / Origin z: 9.404 Å
111213212223313233
T-0.0887 Å20.0137 Å2-0.0033 Å2--0.0787 Å2-0.0109 Å2---0.0879 Å2
L1.5005 °20.1865 °2-0.0482 °2-1.1718 °2-0.0808 °2--1.7473 °2
S-0.0215 Å °-0.0729 Å °0.0397 Å °0.0914 Å °-0.0418 Å °0.0641 Å °-0.0185 Å °-0.0481 Å °0.0634 Å °

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