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- PDB-6jfd: K1U bound crystal structure of class I type b peptide deformylase... -

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Basic information

Entry
Database: PDB / ID: 6jfd
TitleK1U bound crystal structure of class I type b peptide deformylase from Pseudomonas aeruginosa
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 / Peptide deformylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (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: K1U bound crystal structure of class I type b peptide deformylase from Pseudomonas aeruginosa
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 ...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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptide deformylase
B: Peptide deformylase
C: Peptide deformylase
D: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,58111
Polymers75,8874
Non-polymers6957
Water39622
1
A: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0302
Polymers18,9721
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-11 kcal/mol
Surface area8660 Å2
MethodPISA
2
B: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0893
Polymers18,9721
Non-polymers1172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-11 kcal/mol
Surface area8760 Å2
MethodPISA
3
C: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3733
Polymers18,9721
Non-polymers4012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-11 kcal/mol
Surface area8580 Å2
MethodPISA
4
D: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0893
Polymers18,9721
Non-polymers1172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-12 kcal/mol
Surface area8690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.330, 146.356, 65.306
Angle α, β, γ (deg.)90.000, 109.900, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Peptide deformylase / PDF / Polypeptide deformylase


Mass: 18971.656 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAE0831 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A1C7BES9, UniProt: A0A071LDC0*PLUS, peptide deformylase
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 6 / 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.: 22 / 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: 2.77 Å3/Da / Density % sol: 55.56 % / Mosaicity: 1.392 °
Crystal growTemperature: 287 K / Method: evaporation / pH: 8
Details: 0.03M CaCl2, 0.03M MgCl2, 0.1M Sodium Hepes, MOPS pH 8.0, 10.0%(v/v) MPD, 10.0%(w/v) P1k, 10.0%(w/v) PEG 3,350

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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: Jun 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 29213 / % possible obs: 95.1 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.052 / Rrim(I) all: 0.117 / Χ2: 3.011 / Net I/σ(I): 11.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.442.60.44613730.2450.2960.541.24989.4
2.44-2.492.70.42813730.1980.2930.5231.30189.9
2.49-2.532.90.3813700.5410.240.4521.31690.4
2.53-2.5930.36513930.5860.230.4341.47590.1
2.59-2.643.10.34913970.5410.2160.4131.34291.8
2.64-2.73.20.31814050.6930.1950.3761.61793.4
2.7-2.773.40.29414740.8330.1720.3431.77493.4
2.77-2.853.60.25314150.9180.1440.2931.94493
2.85-2.933.80.22914470.9480.1270.2642.14394.8
2.93-3.023.90.20814460.960.1120.2372.26695.3
3.02-3.134.10.18214870.9650.0960.2072.54796.6
3.13-3.264.30.15914910.9810.0820.182.81597.1
3.26-3.414.60.14314990.9830.0710.163.11697.1
3.41-3.584.80.12414820.990.060.1383.55798
3.58-3.814.90.1115220.990.0530.1223.90398.7
3.81-4.15.10.0915390.9930.0430.1014.06498.8
4.1-4.525.20.08315120.9930.0390.0934.14399.1
4.52-5.175.40.07415090.9950.0340.0824.05699
5.17-6.515.60.07515540.9940.0340.0833.86698.8
6.51-505.90.06415250.9960.0280.074.03797.4

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0238refinement
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JF9

6jf9


Resolution: 2.4→49.99 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.866 / SU B: 11.122 / SU ML: 0.247 / SU R Cruickshank DPI: 0.4708 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.471 / ESU R Free: 0.303
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2835 1489 5.1 %RANDOM
Rwork0.2251 ---
obs0.2282 27592 95.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 106.67 Å2 / Biso mean: 40.249 Å2 / Biso min: 13.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0.01 Å2
2--0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 2.4→49.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5048 0 30 22 5100
Biso mean--80.68 28.45 -
Num. residues----639
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195181
X-RAY DIFFRACTIONr_bond_other_d0.0020.024902
X-RAY DIFFRACTIONr_angle_refined_deg1.6921.9847005
X-RAY DIFFRACTIONr_angle_other_deg1.029311345
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.945631
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.73323.016252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.07515882
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7561556
X-RAY DIFFRACTIONr_chiral_restr0.0930.2767
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215739
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021065
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 104 -
Rwork0.343 1924 -
all-2028 -
obs--89.42 %

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