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- PDB-6jfg: K1U bound crystal structure of class II peptide deformylase from ... -

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Basic information

Entry
Database: PDB / ID: 6jfg
TitleK1U 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-K1U / NICKEL (II) ION / Peptide deformylase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLee, I.H. / Ho, T.H. / Kang, L.W.
CitationJournal: To be published
Title: K1U 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 8, 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)20,9903
Polymers20,5891
Non-polymers4012
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-12 kcal/mol
Surface area9500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.908, 120.320, 47.571
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.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-K1U / (3R)-3-benzyl-4-oxo-4-[(2-oxo-2-phenylethyl)sulfanyl]butanoic acid


Mass: 342.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H18O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3.37 Å3/Da / Density % sol: 63.48 %
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: 2.6→50 Å / Num. obs: 8404 / % possible obs: 94.6 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.076 / Rrim(I) all: 0.166 / Χ2: 4.992 / Net I/σ(I): 11.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.643.20.4864300.5840.2970.5731.1996
2.64-2.693.30.4454050.5630.2660.5221.26595.5
2.69-2.743.50.4274300.6880.2530.51.24995.8
2.74-2.83.50.3793900.7510.220.4411.36393.1
2.8-2.863.40.3574050.8110.2130.4181.36194.4
2.86-2.933.60.3244240.850.1890.3771.44496.1
2.93-33.60.2994230.8510.1730.3481.69795.9
3-3.083.90.2684160.9120.1460.3072.17295.4
3.08-3.173.90.2494220.9260.1370.2862.09895.3
3.17-3.284.10.2294040.9430.1230.2612.51395.1
3.28-3.394.30.2094310.90.1150.243.06796.4
3.39-3.534.50.1874050.9540.0950.2113.51294.6
3.53-3.694.50.1654240.9520.0870.1884.74593.6
3.69-3.884.70.1734140.9390.0880.1959.04393.9
3.88-4.134.90.1384240.980.0690.1557.77995.7
4.13-4.4550.1334210.9750.0650.1498.70994.8
4.45-4.894.70.1244310.9790.0610.13911.97994.1
4.89-5.64.90.0984230.990.0470.1096.7294
5.6-7.055.20.0984370.9890.0460.1086.69493
7.05-505.20.0854450.9830.0420.0958.66289.4

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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: 2.6→49.99 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.892 / SU B: 11.465 / SU ML: 0.235 / SU R Cruickshank DPI: 0.439 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.439 / ESU R Free: 0.305
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2653 384 4.6 %RANDOM
Rwork0.1986 ---
obs0.2016 8014 94.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 114.11 Å2 / Biso mean: 45.512 Å2 / Biso min: 18.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0 Å2
2---0.03 Å20 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 2.6→49.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1422 0 25 14 1461
Biso mean--101.08 33.25 -
Num. residues----183
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191473
X-RAY DIFFRACTIONr_bond_other_d0.0020.021369
X-RAY DIFFRACTIONr_angle_refined_deg1.81.9841995
X-RAY DIFFRACTIONr_angle_other_deg1.01933174
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0225182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.34824.62767
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.31715252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.518159
X-RAY DIFFRACTIONr_chiral_restr0.1160.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211637
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02276
LS refinement shellResolution: 2.603→2.67 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.495 26 -
Rwork0.295 597 -
all-623 -
obs--95.11 %

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