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- PDB-6jfq: K2U bound crystal structure of class II peptide deformylase from ... -

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Basic information

Entry
Database: PDB / ID: 6jfq
TitleK2U 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-K2U / NICKEL (II) ION / Peptide deformylase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLee, I.H. / Ho, T.H. / Kang, L.W.
CitationJournal: To be published
Title: K2U 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)21,0633
Polymers20,6881
Non-polymers3752
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-12 kcal/mol
Surface area9680 Å2
Unit cell
Length a, b, c (Å)95.429, 120.699, 47.120
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: 20687.707 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-K2U / (3~{R},4~{R})-4-oxidanyl-3-(phenylmethyl)-4-(phenylmethylsulfanyl)butanoic acid


Mass: 316.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 3.28 Å3/Da / Density % sol: 62.49 % / Mosaicity: 0.812 °
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: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 13884 / % possible obs: 97.4 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.064 / Rrim(I) all: 0.18 / Χ2: 6.604 / Net I/σ(I): 13.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.243.30.4996230.3050.2740.5742.17590
2.24-2.283.70.4386530.5880.2210.4932.45294.2
2.28-2.323.70.4436620.5940.2340.5042.49394.3
2.32-2.373.90.4116630.7670.2060.4622.44793.9
2.37-2.424.20.3996580.7470.1940.4472.54396.1
2.42-2.484.20.3636960.8060.1770.4062.5696.8
2.48-2.544.40.3476650.8150.1690.3882.67596.9
2.54-2.614.90.3086900.8660.1420.3412.9397.9
2.61-2.695.10.2796980.9040.1260.3083.0198.2
2.69-2.775.20.2666950.9550.1170.2923.38498.6
2.77-2.875.40.2486880.9560.1050.273.65197.9
2.87-2.995.70.2136950.9670.0860.234.41197.9
2.99-3.126.50.2097110.9720.080.2255.75298.6
3.12-3.296.90.1886900.970.070.2016.00899.4
3.29-3.497.40.187150.980.0660.1927.6299.2
3.49-3.768.20.1797120.9820.0620.1910.6599.7
3.76-4.148.30.1587210.9870.0550.16712.36199.7
4.14-4.748.50.1357350.9860.0470.14311.37599.9
4.74-5.978.30.1127380.9930.040.1198.11699.3
5.97-508.50.1077760.9910.0380.1149.40798.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LM4

1lm4


Resolution: 2.2→30.78 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.913 / SU B: 7.056 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25192 673 4.9 %RANDOM
Rwork0.20762 ---
obs0.20976 13181 97.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.811 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2---0 Å20 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 2.2→30.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1443 0 23 82 1548
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131492
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171412
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.6592015
X-RAY DIFFRACTIONr_angle_other_deg1.3381.5983285
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5715182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61223.07778
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.46415270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.433159
X-RAY DIFFRACTIONr_chiral_restr0.0830.2196
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021646
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02285
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_it2.6563.497731
X-RAY DIFFRACTIONr_mcbond_other2.6463.497730
X-RAY DIFFRACTIONr_mcangle_it3.9725.24912
X-RAY DIFFRACTIONr_mcangle_other3.9725.24913
X-RAY DIFFRACTIONr_scbond_it3.8334.099761
X-RAY DIFFRACTIONr_scbond_other3.834.104762
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0115.9311104
X-RAY DIFFRACTIONr_long_range_B_refined8.47542.6771611
X-RAY DIFFRACTIONr_long_range_B_other8.47342.6851612
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 46 -
Rwork0.364 896 -
obs--91.72 %

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