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- PDB-6jf5: K2U bound crystal structure of class I type b peptide deformylase... -

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Basic information

Entry
Database: PDB / ID: 6jf5
TitleK2U 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-K2U / Peptide deformylase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLee, I.H. / Ho, T.H. / Kang, L.W.
CitationJournal: To be published
Title: K2U bound crystal structure of class I type b peptide deformylase from Acinetobacter baumannii
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,8986
Polymers35,1342
Non-polymers7644
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-18 kcal/mol
Surface area12980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.072, 76.755, 96.503
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptide deformylase / PDF / Polypeptide deformylase


Mass: 17567.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: def_1, def, def2, def_2, ABUW_2937, APD06_18825, BWP00_08140, C2U32_01090, CBI29_01007, DCD77_14985, DGS69_13130, DOL94_15075, SAMEA104305268_00677, SAMEA104305292_01437, SAMEA104305351_01290
Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A098SKQ8, 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-K2U / (3~{R},4~{R})-4-oxidanyl-3-(phenylmethyl)-4-(phenylmethylsulfanyl)butanoic acid


Mass: 316.415 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H20O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.19 Å3/Da / Density % sol: 43.77 % / Mosaicity: 0.955 °
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: 0.9796 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 20674 / % possible obs: 97.2 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.056 / Rrim(I) all: 0.152 / Χ2: 7.122 / Net I/σ(I): 15.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.034.10.5039750.3790.2540.5681.75792.8
2.03-2.074.30.499770.4540.2410.5491.87794.3
2.07-2.114.50.4359790.6540.2060.4842.06594.5
2.11-2.154.70.39310010.7040.1810.4352.1194.9
2.15-2.24.90.37610110.7730.170.4152.3297
2.2-2.2550.3219920.8950.1450.3542.52796.5
2.25-2.3150.2869990.9190.1260.3142.37895.6
2.31-2.375.40.26910180.9380.1160.2942.58896.6
2.37-2.445.30.24710250.9460.1060.272.73897.3
2.44-2.525.50.2310090.9470.0980.2512.93196.9
2.52-2.615.80.2110250.4830.090.2293.47597.8
2.61-2.716.10.19210470.9730.0780.2083.99997.9
2.71-2.846.50.17310460.9770.0680.1864.79899
2.84-2.996.80.15510320.9790.0590.1665.68698.6
2.99-3.177.10.13810670.9850.0510.1477.15498.7
3.17-3.427.40.12710620.9890.0470.1369.11399.3
3.42-3.767.90.11710680.9880.0430.12412.11699.5
3.76-4.318.50.10410790.9920.0360.1115.47399.5
4.31-5.438.70.08810990.9950.030.09315.9599.5
5.43-508.20.08111630.9950.0290.08612.8997.2

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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: 6JES

6jes


Resolution: 2→29.69 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.494 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.157 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21773 1022 4.9 %RANDOM
Rwork0.18236 ---
obs0.18417 19635 96.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.664 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.02 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 2→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2320 0 46 39 2405
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132406
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172283
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.6533267
X-RAY DIFFRACTIONr_angle_other_deg1.3321.5875284
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.965300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.29823.304115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.58715399
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.0921513
X-RAY DIFFRACTIONr_chiral_restr0.080.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022666
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02465
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_it2.1452.2271209
X-RAY DIFFRACTIONr_mcbond_other2.1272.2241208
X-RAY DIFFRACTIONr_mcangle_it3.2353.3171506
X-RAY DIFFRACTIONr_mcangle_other3.2353.321507
X-RAY DIFFRACTIONr_scbond_it3.7762.8641197
X-RAY DIFFRACTIONr_scbond_other3.7752.8661198
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8874.0951762
X-RAY DIFFRACTIONr_long_range_B_refined7.61627.5322512
X-RAY DIFFRACTIONr_long_range_B_other7.61427.5362513
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 63 -
Rwork0.2 1298 -
obs--86.8 %

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