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- PDB-6jf3: Actinonin bound crystal structure of class I type b peptide defor... -

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Basic information

Entry
Database: PDB / ID: 6jf3
TitleActinonin 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
ACTINONIN / Peptide deformylase / Peptide deformylase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsLee, I.H. / Ho, T.H. / Kang, L.W.
CitationJournal: To be published
Title: Actinonin 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
A: Peptide deformylase
B: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1686
Polymers35,2672
Non-polymers9024
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-97 kcal/mol
Surface area12840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.728, 70.786, 110.859
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-BB2 / ACTINONIN / 2-[(FORMYL-HYDROXY-AMINO)-METHYL]-HEPTANOIC ACID [1-(2-HYDROXYMETHYL-PYRROLIDINE-1-CARBONYL)-2-METHYL-PROPYL]-AMIDE


Mass: 385.498 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H35N3O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: antitumor, antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.37 Å3/Da / Density % sol: 48.13 % / Mosaicity: 0.734 °
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: 11C / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 20895 / % possible obs: 96.7 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.052 / Rrim(I) all: 0.159 / Χ2: 2.544 / Net I/σ(I): 6.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.034.40.4939580.3830.2370.5520.77990.6
2.03-2.074.50.49510060.2220.2380.5550.96792.3
2.07-2.114.90.4579440.3270.2090.5081.11191.7
2.11-2.154.70.4239850.4430.2020.4741.1393
2.15-2.250.3799920.6480.1710.4190.96393
2.2-2.2560.40110180.5490.170.4391.29396.6
2.25-2.316.20.36510380.6890.1460.3961.19797.8
2.31-2.376.70.33410280.8310.1310.3611.11897.3
2.37-2.446.80.31710730.8690.1240.3421.11599
2.44-2.5270.30210480.9040.1150.3251.28698.7
2.52-2.617.40.28210620.8970.1060.3021.33199
2.61-2.717.60.25110420.9320.0930.2691.43397.7
2.71-2.847.40.21810200.9720.080.2331.68695.1
2.84-2.998.90.21110700.9570.070.2232.54999.6
2.99-3.179.50.18910710.9750.0610.1993.11599.8
3.17-3.429.70.16310820.9830.0530.1723.14699.4
3.42-3.76100.14810950.9810.0470.1554.11599.5
3.76-4.319.80.1210590.9890.0390.1264.68795.9
4.31-5.4311.10.10811260.990.0330.1135.00199.6
5.43-5010.10.08111780.9930.0260.0853.8397.5

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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: 2.01→49.99 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.914 / SU B: 5.835 / SU ML: 0.151 / SU R Cruickshank DPI: 0.1942 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.185
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2621 1043 5 %RANDOM
Rwork0.2002 ---
obs0.2032 19817 96.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 98.86 Å2 / Biso mean: 36.177 Å2 / Biso min: 17.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.01→49.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2242 0 56 23 2321
Biso mean--53.29 30.93 -
Num. residues----295
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192326
X-RAY DIFFRACTIONr_bond_other_d0.0020.022236
X-RAY DIFFRACTIONr_angle_refined_deg1.7561.9933149
X-RAY DIFFRACTIONr_angle_other_deg1.0135174
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6635289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.07425.20896
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.13315390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.751512
X-RAY DIFFRACTIONr_chiral_restr0.1090.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212555
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02421
LS refinement shellResolution: 2.008→2.06 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 77 -
Rwork0.348 1310 -
all-1387 -
obs--88.97 %

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