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- PDB-6jf7: K3U bound crystal structure of class I type b peptide deformylase... -

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Basic information

Entry
Database: PDB / ID: 6jf7
TitleK3U bound crystal structure of class I type b peptide deformylase from Acinetobacter baumannii
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 / Peptide deformylase / Peptide deformylase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsJung, K.H. / Ho, T.H. / Lee, I.H. / Kang, L.W.
CitationJournal: To be published
Title: K3U bound crystal structure of class I type b peptide deformylase from Acinetobacter baumannii
Authors: Jung, K.H. / Ho, T.H. / Lee, I.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
B: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1306
Polymers35,2672
Non-polymers8644
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-19 kcal/mol
Surface area13010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.513, 71.259, 110.974
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptide deformylase / PDF / Polypeptide deformylase


Mass: 17633.338 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: def, C3415_07350, IX87_00730 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0E1FIJ3, UniProt: A0A6H2UJ23*PLUS, peptide deformylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-K3U / S-(2-oxo-2-phenylethyl) (2R)-2-benzyl-4,4,4-trifluorobutanethioate


Mass: 366.397 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H17F3O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.33 Å3/Da / Density % sol: 47.11 % / Mosaicity: 0.633 °
Crystal growTemperature: 287 K / Method: evaporation / pH: 6.5
Details: 0.2 M Calcium acetate hydrate, 0.1 M sodium cacodylate trihydrate pH 6.5, 18% (w/v) polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 20960 / % possible obs: 96.4 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.045 / Rrim(I) all: 0.104 / Χ2: 2.288 / Net I/σ(I): 14.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.033.20.3329630.6680.1910.3871.16990.7
2.03-2.073.40.3519810.6690.1970.4051.30990.8
2.07-2.113.50.3259800.7360.180.3741.33494.4
2.11-2.153.70.30510220.7750.1650.3491.43894.5
2.15-2.23.80.27510030.8610.1470.3131.44894.7
2.2-2.254.20.26810390.8670.1390.3031.60496.3
2.25-2.3140.23210180.9360.1210.2631.51594.8
2.31-2.374.20.21310130.9590.1070.2391.59396.8
2.37-2.444.30.20310470.9480.1020.2291.58796.5
2.44-2.524.50.18510400.9720.0920.2081.60297.1
2.52-2.614.70.1710540.9710.0830.191.73197.6
2.61-2.714.70.14510510.9840.070.1621.87998.1
2.71-2.8450.12610590.9880.0580.1392.11597.4
2.84-2.995.10.10710620.9940.050.1192.22698.5
2.99-3.175.40.09910570.9930.0440.1082.94798.3
3.17-3.425.50.08310880.9960.0370.0913.15398.3
3.42-3.765.60.06910840.9960.0310.0763.56598.6
3.76-4.315.70.05510990.9980.0240.063.47298.8
4.31-5.435.80.04611180.9980.020.053.12998.6
5.43-505.80.04511820.9980.0190.0492.95897

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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: 6JES

6jes


Resolution: 2→49.99 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.899 / SU B: 4.617 / SU ML: 0.126 / SU R Cruickshank DPI: 0.1906 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.177
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2478 1032 4.9 %RANDOM
Rwork0.1922 ---
obs0.195 19904 96.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 80.22 Å2 / Biso mean: 25.762 Å2 / Biso min: 10.68 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2→49.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2307 0 52 27 2386
Biso mean--42.46 22.08 -
Num. residues----303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192394
X-RAY DIFFRACTIONr_bond_other_d0.0020.022271
X-RAY DIFFRACTIONr_angle_refined_deg1.9141.9953246
X-RAY DIFFRACTIONr_angle_other_deg1.04935253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.365298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.12125100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.8415400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2231514
X-RAY DIFFRACTIONr_chiral_restr0.1960.2379
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212632
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02446
LS refinement shellResolution: 2.004→2.056 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 73 -
Rwork0.254 1271 -
all-1344 -
obs--84.74 %

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