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- PDB-5jey: Crystal structure of type 2 PDF from Streptococcus agalactiae, cr... -

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Basic information

Entry
Database: PDB / ID: 5jey
TitleCrystal structure of type 2 PDF from Streptococcus agalactiae, crystallized in cacodylate buffer
ComponentsPeptide deformylase
KeywordsHYDROLASE / PDF / type 2 / NME / N-terminal methionine excision / Streptococcus agalactiae / inhibitor
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
NICKEL (II) ION / Peptide deformylase
Similarity search - Component
Biological speciesStreptococcus agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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_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)23,3649
Polymers22,8941
Non-polymers4708
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-55 kcal/mol
Surface area10880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.360, 65.980, 89.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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 / Plasmid: pET16b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 pLysS / References: UniProt: Q8E378, peptide deformylase
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.67 Å3/Da / Density % sol: 53.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 9% PEG-8000, 100mM Na Cacodylate pH6.5, 100mM Zn acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 28, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.78→50 Å / Num. obs: 11619 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.55 % / Rsym value: 0.159 / Net I/σ(I): 8.8
Reflection shellResolution: 2.78→2.95 Å / Redundancy: 2.44 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.43 / % possible all: 93.2

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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: 2.8→37.53 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.866 / SU B: 13.37 / SU ML: 0.262 / Cross valid method: THROUGHOUT / ESU R Free: 0.373 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24787 320 5 %RANDOM
Rwork0.18197 ---
obs0.18535 6079 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.437 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å20 Å20 Å2
2--0.86 Å20 Å2
3----0.13 Å2
Refinement stepCycle: 1 / Resolution: 2.8→37.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1567 0 8 124 1699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0221593
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.6061.9772158
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.235202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.30925.14370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.32315284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg31.881158
X-RAY DIFFRACTIONr_chiral_restr0.1370.2247
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021189
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2510.2668
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3310.21069
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2210.281
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1470.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2630.218
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4150.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5561.51051
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.48521627
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.9083614
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.7824.5531
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: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 23 -
Rwork0.315 437 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -7.277 Å / Origin y: -6.849 Å / Origin z: 9.576 Å
111213212223313233
T0.1185 Å20.0026 Å2-0.0132 Å2-0.0412 Å2-0.0003 Å2--0.0389 Å2
L2.054 °20.4153 °2-0.0512 °2-1.6623 °20.1098 °2--1.7449 °2
S-0.0099 Å °-0.1477 Å °0.1278 Å °0.1344 Å °-0.0288 Å °0.0465 Å °-0.0602 Å °0.0108 Å °0.0386 Å °

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