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- PDB-6jf9: Apo crystal structure of class I type b peptide deformylase from ... -

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Basic information

Entry
Database: PDB / ID: 6jf9
TitleApo 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
NICKEL (II) ION / Peptide deformylase / Peptide deformylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLee, I.H. / Ho, T.H. / Kang, L.W.
CitationJournal: To be published
Title: Apo crystal structure of class I type b peptide deformylase from Pseudomonas aeruginosa
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 / 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)38,6415
Polymers38,4322
Non-polymers2093
Water1,11762
1
A: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2752
Polymers19,2161
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-11 kcal/mol
Surface area8320 Å2
MethodPISA
2
B: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3673
Polymers19,2161
Non-polymers1512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-11 kcal/mol
Surface area8770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.486, 122.045, 149.380
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: 19215.947 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.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.78 Å3/Da / Density % sol: 55.74 % / Mosaicity: 0.399 °
Crystal growTemperature: 287 K / Method: evaporation / pH: 8
Details: 0.03 M CaCl2, 0.03 M MgCl2, 0.1 M 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: 1.7→50 Å / Num. obs: 41544 / % possible obs: 92.1 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.032 / Rrim(I) all: 0.108 / Χ2: 8.767 / Net I/σ(I): 22.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.7312.70.4220450.9570.1180.4377.50893
1.73-1.7613.50.24820850.9870.0690.2582.29892.8
1.76-1.7913.50.20820710.9920.0580.2172.3893.2
1.79-1.8313.40.17820630.9870.050.1852.63894
1.83-1.87130.1820950.9930.0510.1873.25293.7
1.87-1.919.20.35621170.8510.1220.37924.70793.5
1.91-1.969.30.29120600.8690.0930.30717.53792.8
1.96-2.0212.80.1221540.9950.0350.1254.79396.5
2.02-2.078.70.18719730.9120.0740.20310.3489
2.07-2.1411.10.11421800.9940.0350.1197.58497.2
2.14-2.2212.90.122260.9960.0290.1046.90298.9
2.22-2.319.50.16421050.9390.0590.17611.79193.5
2.31-2.4113.20.08622190.9970.0250.097.09299.8
2.41-2.5413.20.08222430.9970.0230.0867.47999.7
2.54-2.711.40.09722360.990.0310.10210.35398.1
2.7-2.9113.30.08222610.9950.0230.0859.47799.8
2.91-3.213.40.08922660.9930.0260.09212.35699.9
3.2-3.6610.10.09116630.9920.0290.09615.59972.5
3.66-4.61100.07314530.9950.0240.07712.58662.7
4.61-5011.50.07420290.9950.0230.07713.57183.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0238refinement
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5vcp

5vcp


Resolution: 1.7→49.99 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.883 / SU B: 2.619 / SU ML: 0.087 / SU R Cruickshank DPI: 0.1296 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.128
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2807 2057 5 %RANDOM
Rwork0.2431 ---
obs0.2449 39304 91.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 70.36 Å2 / Biso mean: 24.16 Å2 / Biso min: 11.87 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.7→49.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2521 0 8 62 2591
Biso mean--44.51 23.22 -
Num. residues----321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192581
X-RAY DIFFRACTIONr_bond_other_d0.0020.022445
X-RAY DIFFRACTIONr_angle_refined_deg2.1071.9823492
X-RAY DIFFRACTIONr_angle_other_deg1.1435658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3355317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.30723.008123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.69815435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8491527
X-RAY DIFFRACTIONr_chiral_restr0.1520.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212855
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02524
LS refinement shellResolution: 1.702→1.746 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 143 -
Rwork0.325 2804 -
all-2947 -
obs--90.01 %

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