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- PDB-6jfn: K4U bound crystal structure of class I type b peptide deformylase... -

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Basic information

Entry
Database: PDB / ID: 6jfn
TitleK4U bound crystal structure of class I type b peptide deformylase from Pseudomonas aeruginosa
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 / NICKEL (II) ION / Peptide deformylase / Peptide deformylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsLee, I.H. / Ho, T.H. / Kang, L.W.
CitationJournal: To be published
Title: K4U bound crystal structure of class I type b peptide deformylase from Pseudomonas aeruginosa
Authors: Lee, I.H. / Ho, T.H. / Kang, L.W.
History
DepositionFeb 11, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 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 / _struct_conn.ptnr2_symmetry

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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)39,0626
Polymers38,6622
Non-polymers4004
Water34219
1
A: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4483
Polymers19,3311
Non-polymers1172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-17 kcal/mol
Surface area9210 Å2
MethodPISA
2
B: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6143
Polymers19,3311
Non-polymers2832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-12 kcal/mol
Surface area8310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.147, 122.026, 146.621
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Peptide deformylase


Mass: 19331.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAE0831 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A1C7BES9, UniProt: A0A071LDC0*PLUS, peptide deformylase
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#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.: 19 / 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: 2.64 Å3/Da / Density % sol: 53.34 % / Mosaicity: 1.027 °
Crystal growTemperature: 287 K / Method: evaporation / pH: 8
Details: 0.03M CaCl2, 0.03M MgCl2, 0.1M Sodium Hepes, MOPS pH 8.0, 10.0%(v/v) MPD, 10.0%(w/v) P1k, 10.0%(w/v) PEG 3,350

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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: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. obs: 25841 / % possible obs: 99.8 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.178 / Rpim(I) all: 0.057 / Rrim(I) all: 0.187 / Χ2: 9.999 / Net I/σ(I): 10.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.04-2.0870.49612380.9330.1880.5321.92598.6
2.08-2.117.90.48212820.9540.1750.5142.25499.8
2.11-2.158.40.46812730.9480.1680.4982.33199.8
2.15-2.28.80.46112800.9440.1620.4892.36999.9
2.2-2.259.20.41412630.9530.1430.4392.987100
2.25-2.39.60.38412740.970.1290.4063.542100
2.3-2.359.80.39512660.9760.1310.4173.204100
2.35-2.429.90.38112880.9640.1260.4023.87499.9
2.42-2.49100.34812830.960.1150.3674.299100
2.49-2.5710.50.32812840.9690.1050.3445.35899.9
2.57-2.6610.50.29512560.980.0950.315.958100
2.66-2.7710.90.27613200.9830.0870.296.912100
2.77-2.8911.30.25912660.9810.080.2719.33199.9
2.89-3.0511.50.24212870.9890.0750.25310.823100
3.05-3.2411.90.22113210.980.0670.23113.343100
3.24-3.4912.40.2112800.980.0630.2217.17499.9
3.49-3.8412.40.19213160.9740.0590.20121.904100
3.84-4.3911.90.17613200.9860.0570.18524.308100
4.39-5.5411.70.14613440.9790.0470.15420.274100
5.54-50120.11314000.9880.0360.11915.8599.1

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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: 6JF9

6jf9


Resolution: 2.04→31.66 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.911 / SU B: 7.164 / SU ML: 0.187 / SU R Cruickshank DPI: 0.2198 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.196
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2901 1267 4.9 %RANDOM
Rwork0.2465 ---
obs0.2487 24457 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 108.87 Å2 / Biso mean: 45.159 Å2 / Biso min: 26.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.03 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 2.04→31.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2559 0 19 19 2597
Biso mean--83.17 38.52 -
Num. residues----325
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132631
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172477
X-RAY DIFFRACTIONr_angle_refined_deg1.7271.6523559
X-RAY DIFFRACTIONr_angle_other_deg1.5271.5775734
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8195321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.10520.844154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.67415442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4851527
X-RAY DIFFRACTIONr_chiral_restr0.0860.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022950
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02569
LS refinement shellResolution: 2.04→2.093 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.444 92 -
Rwork0.428 1779 -
all-1871 -
obs--99.63 %

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