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- PDB-6jex: K4U bound crystal peptide deformylase from Acinetobacter baumanii -

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Basic information

Entry
Database: PDB / ID: 6jex
TitleK4U bound crystal peptide deformylase from Acinetobacter baumanii
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
L-[(N-HYDROXYAMINO)CARBONYL]PHENYLALANINE / Peptide deformylase / Peptide deformylase
Similarity search - Component
Biological speciesAcinetobacter baumannii MRSN 3527 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsLee, I.H. / Ho, T.H. / Kang, L.W.
CitationJournal: To be published
Title: K4U bound crystal peptide deformylase from Acinetobacter baumanii
Authors: Lee, I.H. / Ho, T.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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)39,5105
Polymers39,1552
Non-polymers3553
Water1,874104
1
A: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6432
Polymers19,5781
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-39 kcal/mol
Surface area8990 Å2
MethodPISA
2
B: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8673
Polymers19,5781
Non-polymers2902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.176, 40.176, 187.645
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Peptide deformylase / PDF / Polypeptide deformylase


Mass: 19577.525 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,K0420859 / 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-LHY / L-[(N-HYDROXYAMINO)CARBONYL]PHENYLALANINE


Mass: 224.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.23 Å3/Da / Density % sol: 44.92 % / Mosaicity: 0.381 °
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: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 19227 / % possible obs: 98.2 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.075 / Rrim(I) all: 0.129 / Χ2: 12.944 / 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
2.1-2.142.80.3169400.830.2250.3894.113100
2.14-2.182.80.2799830.8810.1980.3434.747100
2.18-2.222.90.26810190.880.1910.335.554100
2.22-2.262.90.2319490.8990.1620.2826.974100
2.26-2.312.90.2219780.9180.1560.2727.09199.7
2.31-2.372.90.2219970.8860.1570.2718.124100
2.37-2.422.80.1929240.9310.1350.2369.592100
2.42-2.492.90.18710230.9260.1310.2299.714100
2.49-2.562.90.1619640.9450.1120.19710.08999.8
2.56-2.652.90.15610040.950.1080.1910.303100
2.65-2.742.90.1479370.9470.1020.17913.135100
2.74-2.852.90.13810290.9550.0960.16913.248100
2.85-2.982.90.1269310.9680.0880.15415.1100
2.98-3.142.90.1179810.970.0820.14317.048100
3.14-3.332.90.10410160.9640.0730.12717.519100
3.33-3.592.80.0929620.9740.0650.11318.82399.8
3.59-3.952.80.0879330.9710.0630.10819.03197.2
3.95-4.522.60.0789030.9810.0590.09822.4390.5
4.52-5.72.60.0668920.9840.0480.08228.2989.8
5.7-502.70.0738620.9770.0530.09126.5787.8

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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: 2.11→49.99 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.899 / SU B: 5.516 / SU ML: 0.148 / SU R Cruickshank DPI: 0.2594 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.259 / ESU R Free: 0.227
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2721 1053 5.5 %RANDOM
Rwork0.1971 ---
obs0.2011 18121 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 94.95 Å2 / Biso mean: 36.625 Å2 / Biso min: 19.68 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 2.11→49.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2584 0 18 104 2706
Biso mean--53.23 44.51 -
Num. residues----344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192646
X-RAY DIFFRACTIONr_bond_other_d0.0020.022495
X-RAY DIFFRACTIONr_angle_refined_deg1.8941.9953603
X-RAY DIFFRACTIONr_angle_other_deg1.18435757
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.565342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.10824.667105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.74315428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0991516
X-RAY DIFFRACTIONr_chiral_restr0.1250.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212933
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02485
LS refinement shellResolution: 2.108→2.163 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 76 -
Rwork0.213 1341 -
all-1417 -
obs--99.72 %

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