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- PDB-3u7k: Crystal structures of the Staphylococcus aureus peptide deformyla... -

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Basic information

Entry
Database: PDB / ID: 3u7k
TitleCrystal structures of the Staphylococcus aureus peptide deformylase in complex with two classes of new inhibitors
ComponentsPeptide deformylase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PDF-INHIBITOR / PDF / PEPTIDE DEFORMYLASE / HYDROLASE / 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-MDB / Peptide deformylase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLee, S.J. / Lee, S.-J. / Lee, S.K. / Yoon, H.-J. / Lee, H.H. / Kim, K.K. / Lee, B.J. / Suh, S.W.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structures of Staphylococcus aureus peptide deformylase in complex with two classes of new inhibitors
Authors: Lee, S.J. / Lee, S.-J. / Lee, S.K. / Yoon, H.-J. / Lee, H.H. / Kim, K.K. / Lee, B.J. / Lee, B.I. / Suh, S.W.
History
DepositionOct 14, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Nov 1, 2023Group: 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_ref_seq_dif / 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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1933
Polymers21,6931
Non-polymers5002
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.776, 120.269, 47.753
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Peptide deformylase / PDF / Polypeptide deformylase


Mass: 21692.713 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: COL / Gene: SACOL1100 / Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q5HGZ3, peptide deformylase
#2: Chemical ChemComp-MDB / (S)-N-(cyclopentylmethyl)-N-(2-(hydroxyamino)-2-oxoethyl)-2-(3-(2-methoxyphenyl)ureido)-3,3-dimethylbutanamide


Mass: 434.529 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H34N4O5
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.1 Å3/Da / Density % sol: 60.37 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 23%(w/v) PEG 4000, 50mM Tris-HCl, 15%(v/v) glycerol, 100mM MgCl2, 20mM CaCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9722 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jun 21, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9722 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 21933 / % possible obs: 99.9 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q1Y

1q1y


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.877 / SU B: 2.914 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26609 1093 5.1 %RANDOM
Rwork0.21369 ---
obs0.21623 20500 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.702 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å20 Å20 Å2
2---1.63 Å20 Å2
3---0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1462 0 32 203 1697
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221520
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.33422056
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6995184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.20724.85770
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59315273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.201159
X-RAY DIFFRACTIONr_chiral_restr0.0760.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211135
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6331.5927
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.19321506
X-RAY DIFFRACTIONr_scbond_it1.9543593
X-RAY DIFFRACTIONr_scangle_it3.3444.5550
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 74 -
Rwork0.245 1485 -
obs--99.87 %

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