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- PDB-6jet: Actinonin bound crystal structure of class I type a peptide defor... -

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Basic information

Entry
Database: PDB / ID: 6jet
TitleActinonin bound crystal structure of class I type a 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 MRSN 3527 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHo, T.H. / Lee, I.H. / Kang, L.W.
CitationJournal: To be published
Title: Actinonin bound crystal structure of class I type a peptide deformylase from Acinetobacter baumannii
Authors: Ho, T.H. / Lee, I.H. / Kang, L.W.
History
DepositionFeb 7, 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)39,9156
Polymers39,0132
Non-polymers9024
Water1,00956
1
A: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9573
Polymers19,5061
Non-polymers4512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-41 kcal/mol
Surface area8570 Å2
MethodPISA
2
B: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9573
Polymers19,5061
Non-polymers4512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-41 kcal/mol
Surface area8760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.666, 112.903, 43.678
Angle α, β, γ (deg.)90.000, 102.850, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Peptide deformylase / PDF / Polypeptide deformylase


Mass: 19506.447 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii MRSN 3527 (bacteria)
Gene: def_1, def, T630_0214 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0J1A8B1, UniProt: B0VNL8*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.: 56 / 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: 2.69 Å3/Da / Density % sol: 54.29 % / Mosaicity: 0.842 °
Crystal growTemperature: 287 K / Method: evaporation / pH: 8.5
Details: 0.03 M MgCl2, 0.03 M CaCl2, 15% (v/v) PEGMME, 15% (w/v) PEG 20000, 0.1 M Tris (base)/ Bicine pH 8.5

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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: May 31, 2015
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: 16034 / % possible obs: 99.8 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.043 / Rrim(I) all: 0.117 / Χ2: 9.069 / Net I/σ(I): 21.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.447.60.228010.9740.0850.2364.023100
2.44-2.497.60.217740.9760.0820.2264.234100
2.49-2.537.60.1838310.9850.0710.1974.504100
2.53-2.597.60.198100.9840.0730.2044.342100
2.59-2.647.70.1697710.9820.0650.1815.101100
2.64-2.77.60.168260.9860.0630.1725.281100
2.7-2.777.60.1617740.9780.0630.1736.022100
2.77-2.857.60.1538210.9850.0590.1646.393100
2.85-2.937.70.147980.9750.0550.156.987100
2.93-3.027.70.1737920.9880.0670.1858.698100
3.02-3.137.60.1258210.9890.0490.1348.871100
3.13-3.267.70.1227780.9890.0470.1310.036100
3.26-3.417.60.1158190.9880.0450.12311.3100
3.41-3.587.60.18000.9910.0390.10810.457100
3.58-3.817.60.0967790.9910.0380.10311.56699.9
3.81-4.17.50.0938030.9910.0370.112.32399.9
4.1-4.527.30.098070.9910.0360.09712.73298.8
4.52-5.177.30.0947910.9860.0380.10113.74799.1
5.17-6.517.30.0888120.9910.0350.09514.46299.6
6.51-507.20.0888260.990.0360.09521.46198.2

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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: 6JER

6jer


Resolution: 2.6→49.99 Å / Cor.coef. Fo:Fc: 0.866 / Cor.coef. Fo:Fc free: 0.832 / SU B: 14.834 / SU ML: 0.322 / SU R Cruickshank DPI: 0.8874 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.887 / ESU R Free: 0.367
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2951 646 5.1 %RANDOM
Rwork0.247 ---
obs0.2496 12044 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 77.73 Å2 / Biso mean: 31.901 Å2 / Biso min: 5.77 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2---0.01 Å2-0 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.6→49.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2539 0 56 56 2651
Biso mean--40.85 28.24 -
Num. residues----341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192639
X-RAY DIFFRACTIONr_bond_other_d0.0060.022493
X-RAY DIFFRACTIONr_angle_refined_deg1.6962.0093596
X-RAY DIFFRACTIONr_angle_other_deg1.05335755
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6015339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.83824.8100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.82215411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9461514
X-RAY DIFFRACTIONr_chiral_restr0.0850.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212913
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02473
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 33 -
Rwork0.235 899 -
all-932 -
obs--100 %

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