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- PDB-5jf4: Crystal structure of type 2 PDF from Streptococcus agalactiae in ... -

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Basic information

Entry
Database: PDB / ID: 5jf4
TitleCrystal structure of type 2 PDF from Streptococcus agalactiae in complex with inhibitor AT019
ComponentsPeptide deformylase
KeywordsHYDROLASE / PDF / type 2 / NME / N-terminal methionine excision / Streptococcus agalactiae / inhibitor / AT019
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-6JT / ACETATE ION / IMIDAZOLE / Peptide deformylase
Similarity search - Component
Biological speciesStreptococcus agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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)23,98113
Polymers22,8941
Non-polymers1,08612
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-187 kcal/mol
Surface area10590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.150, 65.710, 88.540
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, 205 molecules

#2: Chemical ChemComp-6JT / (3R)-3-{3-[(1-benzofuran-3-yl)methyl]-1,2,4-oxadiazol-5-yl}-4-cyclopentyl-N-hydroxybutanamide


Mass: 369.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N3O4
#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.: 193 / 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: 52.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 7% PEG-8000, 100mM imidazole pH7.5, 400mM 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: 2.4→50 Å / Num. obs: 18118 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.49 % / CC1/2: 0.987 / Rsym value: 0.183 / Net I/σ(I): 8.88
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 5.09 % / Rmerge(I) obs: 0.783 / Mean I/σ(I) obs: 3.15 / % possible all: 99.9

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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: 2.4→44.28 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.906 / SU B: 6.804 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.363 / ESU R Free: 0.241 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22517 494 5 %RANDOM
Rwork0.16198 ---
obs0.16517 9374 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.215 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å20 Å2
2--0.6 Å20 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.4→44.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1581 0 35 193 1809
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221633
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8751.9912206
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9655202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.38925.06873
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.28415291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.316159
X-RAY DIFFRACTIONr_chiral_restr0.1190.2249
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021223
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.2666
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21067
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2570.2125
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1750.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3030.225
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0191.51042
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.76221632
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0673646
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.9724.5574
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: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 35 -
Rwork0.221 667 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -7.321 Å / Origin y: -6.837 Å / Origin z: 9.49 Å
111213212223313233
T-0.06 Å20.0097 Å2-0.0152 Å2--0.0757 Å20.0049 Å2---0.0861 Å2
L1.6216 °20.2282 °2-0.2142 °2-0.972 °2-0.0112 °2--1.4804 °2
S-0.0396 Å °-0.1279 Å °0.1189 Å °0.0772 Å °-0.018 Å °0.0484 Å °-0.0858 Å °-0.0323 Å °0.0575 Å °

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