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- PDB-6jfr: K3U bound crystal structure of class II peptide deformylase from ... -

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Basic information

Entry
Database: PDB / ID: 6jfr
TitleK3U bound crystal structure of class II peptide deformylase from methicillin resistant Staphylococcus aureus
ComponentsPeptide deformylase
KeywordsHYDROLASE / peptide deformylase
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-K3U / NICKEL (II) ION / Peptide deformylase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLee, I.H. / Ho, T.H. / Kang, L.W.
CitationJournal: To be published
Title: K3U bound crystal structure of class II peptide deformylase from methicillin resistant Staphylococcus aureus
Authors: Lee, I.H. / Ho, T.H. / Kang, L.W.
History
DepositionFeb 11, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)21,0724
Polymers20,5891
Non-polymers4843
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-7 kcal/mol
Surface area9270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.792, 120.709, 47.281
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Peptide deformylase / PDF / Polypeptide deformylase


Mass: 20588.576 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: CCARM3089 / Gene: def, def1, pdf1 / Plasmid: pET29b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P68826, peptide deformylase
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-K3U / S-(2-oxo-2-phenylethyl) (2R)-2-benzyl-4,4,4-trifluorobutanethioate


Mass: 366.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H17F3O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 3.32 Å3/Da / Density % sol: 62.94 %
Crystal growTemperature: 287 K / Method: evaporation / pH: 8.5
Details: 0.02M CaCl2, 0.1M MgCl2, 15% (v/v) Glycerol, 25% (w/v) PEG 4K, 0.05M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 10475 / % possible obs: 94.7 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.052 / Rrim(I) all: 0.132 / Χ2: 6.366 / Net I/σ(I): 16.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.442.90.2664820.7920.1620.3131.97788.6
2.44-2.4930.2564850.7650.1540.3012.19188
2.49-2.5330.2444740.8150.1450.2872.08391.2
2.53-2.593.30.2315080.8590.1330.2692.21891.2
2.59-2.643.40.2164910.8760.1210.2492.28189.4
2.64-2.73.60.2044650.8890.1110.2342.45491.2
2.7-2.773.60.2015080.9370.1090.232.70991.7
2.77-2.853.70.1755040.9460.0920.1992.53691.6
2.85-2.933.90.1665130.9650.0840.1873.24293.4
2.93-3.024.40.1525130.9720.0730.173.52294.5
3.02-3.134.60.1455320.9790.0670.163.78296
3.13-3.264.90.1385130.9840.0630.1524.05995.5
3.26-3.415.30.1345440.9810.0590.1475.24297.8
3.41-3.585.70.1275510.9810.0540.1385.92198.7
3.58-3.816.10.135460.9880.0540.1418.34198.9
3.81-4.16.20.1355530.9860.0540.14511.49499.5
4.1-4.526.50.125630.9850.0480.12912.36499.1
4.52-5.176.50.1025560.9920.0410.119.76399.1
5.17-6.516.50.0915680.9920.0370.0987.41498.6
6.51-506.70.0846060.9950.0330.098.4697.4

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0158refinement
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LM4

1lm4


Resolution: 2.4→49.99 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.886 / SU B: 8.215 / SU ML: 0.181 / SU R Cruickshank DPI: 0.296 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.296 / ESU R Free: 0.242
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2543 541 5.2 %RANDOM
Rwork0.1999 ---
obs0.2026 9930 94.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 100.3 Å2 / Biso mean: 35.356 Å2 / Biso min: 17.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 2.4→49.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1409 0 27 18 1454
Biso mean--86.66 30.72 -
Num. residues----183
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191461
X-RAY DIFFRACTIONr_bond_other_d0.0020.021351
X-RAY DIFFRACTIONr_angle_refined_deg1.8061.9831983
X-RAY DIFFRACTIONr_angle_other_deg1.03533126
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9495182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.49724.46265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.34415243
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.454159
X-RAY DIFFRACTIONr_chiral_restr0.1010.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211625
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02276
LS refinement shellResolution: 2.402→2.465 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 27 -
Rwork0.338 667 -
all-694 -
obs--87.41 %

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