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- PDB-6jer: Apo crystal structure of class I type a peptide deformylase from ... -

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Basic information

Entry
Database: PDB / ID: 6jer
TitleApo 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 / co-translational protein modification / 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
Peptide deformylase / Peptide deformylase
Similarity search - Component
Biological speciesAcinetobacter baumannii MRSN 3527 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHo, T.H. / Lee, I.H. / Kang, L.W.
CitationJournal: Biodesign / Year: 2017
Title: Expression, crystallization, and preliminary X-ray crystallographic analysis of peptide deformylase from Acinetobacter baumanii
Authors: 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

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Assembly

Deposited unit
A: Peptide deformylase
B: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0024
Polymers38,8712
Non-polymers1312
Water1267
1
A: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5012
Polymers19,4351
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-38 kcal/mol
Surface area9780 Å2
MethodPISA
2
B: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5012
Polymers19,4351
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-38 kcal/mol
Surface area9700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.425, 39.425, 187.888
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: 19435.369 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.15 Å3/Da / Density % sol: 42.87 % / Mosaicity: 0.808 °
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: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 28, 2014
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: 18672 / % possible obs: 97.6 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.065 / Rrim(I) all: 0.116 / Χ2: 4.094 / Net I/σ(I): 12.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.443.70.39210090.890.240.4612.10999.9
2.44-2.493.70.3349080.8890.2060.3932.67799.9
2.49-2.533.70.3259210.9010.1970.382.40799.6
2.53-2.593.70.2739940.9260.1690.3222.513100
2.59-2.643.60.2669420.930.1640.3132.785100
2.64-2.73.60.2369210.9320.1460.2783.00799.9
2.7-2.773.60.2049720.950.1280.2413.13499.8
2.77-2.853.60.1929490.9640.1210.2273.27299.7
2.85-2.933.60.179140.9620.1080.2023.59199.6
2.93-3.023.50.15910180.9660.1010.1893.799.6
3.02-3.133.40.1358920.9730.0880.1614.11699.3
3.13-3.263.40.11610090.9790.0770.1394.27198.8
3.26-3.413.30.1028840.9790.0690.1234.62799
3.41-3.583.20.0919800.9830.0630.1115.26197.9
3.58-3.813.10.0878960.9820.060.1065.33597
3.81-4.12.80.0748740.9820.0540.0927.23194.1
4.1-4.522.80.0698950.9850.0520.0875.4889.9
4.52-5.172.80.0658590.9830.0490.0825.9791.2
5.17-6.5130.0659530.9860.0460.085.63896.5
6.51-502.90.0598820.9870.0430.07310.07491.6

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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: 1S17

1s17


Resolution: 2.4→34.17 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.909 / WRfactor Rfree: 0.3016 / WRfactor Rwork: 0.2258 / FOM work R set: 0.7807 / SU B: 10.105 / SU ML: 0.234 / SU R Cruickshank DPI: 0.9399 / SU Rfree: 0.3425 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.94 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2891 578 4.7 %RANDOM
Rwork0.2207 ---
obs0.2238 11805 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.66 Å2 / Biso mean: 50.8 Å2 / Biso min: 26.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å2-0 Å2
2---0.04 Å2-0 Å2
3---0.13 Å2
Refinement stepCycle: final / Resolution: 2.4→34.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2714 0 2 7 2723
Biso mean--42.85 43.98 -
Num. residues----340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132760
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172678
X-RAY DIFFRACTIONr_angle_refined_deg1.6771.6533734
X-RAY DIFFRACTIONr_angle_other_deg1.2111.5766228
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2225338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.55422.208154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.89515520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1041524
X-RAY DIFFRACTIONr_chiral_restr0.080.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023032
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02528
LS refinement shellResolution: 2.401→2.463 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 38 -
Rwork0.305 947 -
all-985 -
obs--98.7 %

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