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- PDB-6jf4: K1U bound crystal structure of class I type b peptide deformylase... -

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Basic information

Entry
Database: PDB / ID: 6jf4
TitleK1U 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-K1U / 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: K1U 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)35,9506
Polymers35,1342
Non-polymers8164
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-19 kcal/mol
Surface area12980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.967, 77.351, 96.582
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-K1U / (3R)-3-benzyl-4-oxo-4-[(2-oxo-2-phenylethyl)sulfanyl]butanoic acid


Mass: 342.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H18O4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.27 Å3/Da / Density % sol: 45.91 % / Mosaicity: 0.718 °
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: 20689 / % possible obs: 96.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.051 / Rrim(I) all: 0.149 / Χ2: 7.431 / Net I/σ(I): 16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.033.90.4619830.3750.2390.5242.23992.3
2.03-2.074.10.4349710.320.2230.4922.24694
2.07-2.114.40.3969810.5190.1940.4442.43494.7
2.11-2.154.60.36210080.6550.1730.4042.60294.5
2.15-2.250.35110080.7410.1580.3872.88596.7
2.2-2.255.40.29710030.8590.1270.3252.99695.9
2.25-2.315.30.2689970.9010.1150.2933.07495.4
2.31-2.375.60.2510100.9420.1040.2723.08496.1
2.37-2.445.80.22610180.9450.0940.2463.24296.4
2.44-2.525.90.20310250.9630.0820.223.36296.8
2.52-2.616.40.18810270.9640.0730.2033.89897.3
2.61-2.716.60.16810380.9760.0640.1814.25898.5
2.71-2.847.20.16110550.9770.0590.1725.43498
2.84-2.997.50.1610350.9770.0570.177.06297.6
2.99-3.178.20.15110650.9830.0520.168.72498.3
3.17-3.428.60.15110580.9830.0520.1611.34598.5
3.42-3.769.30.13110640.9840.0430.13812.71498.9
3.76-4.319.30.11310760.9910.0380.11913.85898.7
4.31-5.439.90.09510970.9950.030.111.84399
5.43-509.50.09711700.9910.0320.10212.10997.3

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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→33.92 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.905 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22532 1013 4.9 %RANDOM
Rwork0.1832 ---
obs0.18523 19662 96.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.482 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 2→33.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2303 0 50 44 2397
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132390
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172270
X-RAY DIFFRACTIONr_angle_refined_deg1.6921.6553241
X-RAY DIFFRACTIONr_angle_other_deg1.3531.5855253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1165297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.76923.333114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.0815400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8571513
X-RAY DIFFRACTIONr_chiral_restr0.1080.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022651
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02460
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_it2.0212.4271200
X-RAY DIFFRACTIONr_mcbond_other2.0212.4251199
X-RAY DIFFRACTIONr_mcangle_it3.0093.6151493
X-RAY DIFFRACTIONr_mcangle_other3.0083.6171494
X-RAY DIFFRACTIONr_scbond_it3.7473.071190
X-RAY DIFFRACTIONr_scbond_other3.7463.0721191
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9114.4041749
X-RAY DIFFRACTIONr_long_range_B_refined7.60429.7032477
X-RAY DIFFRACTIONr_long_range_B_other7.60329.7082478
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
Rfree0.231 63 -
Rwork0.229 1289 -
obs--85.9 %

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