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- PDB-2os1: Structures of actinonin bound peptide deformylases from E. faecal... -

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Basic information

Entry
Database: PDB / ID: 2os1
TitleStructures of actinonin bound peptide deformylases from E. faecalis and S. pyogenes
ComponentsPeptide deformylase
KeywordsHYDROLASE / PDF / 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 / NICKEL (II) ION / Peptide deformylase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKim, E.E. / Kim, K.-H. / Moon, J.H. / Choi, K. / Lee, H.K. / Park, H.S.
CitationJournal: To be Published
Title: Structures of actinonin bound peptide deformylases from E. faecalis and S. pyogenes
Authors: Kim, E.E. / Kim, K.-H. / Moon, J.H. / Choi, K. / Lee, H.K. / Park, H.S.
History
DepositionFeb 5, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7836
Polymers21,0511
Non-polymers7325
Water3,783210
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.999, 67.999, 41.127
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Peptide deformylase / PDF / Polypeptide deformylase


Mass: 21051.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: ATCC 700802 / Gene: def / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q82ZJ0, peptide deformylase
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: 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.: 1 / Source method: obtained synthetically / Formula: C19H35N3O5 / Comment: antibiotic*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.26 Å3/Da / Density % sol: 45.51 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 16% PEG 8000, 0.2M Ammonium sulfate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1.12714 Å
DetectorType: BRUKER PROTEUM 300 / Detector: CCD / Date: Nov 26, 2004 / Details: mirrors
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12714 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 37104 / % possible obs: 86.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 11.9 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 28.3
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 4.5 / % possible all: 19.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LQY

1lqy


Resolution: 1.5→24.04 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 336726.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.198 1443 5 %RANDOM
Rwork0.186 ---
obs0.186 28932 95.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.0861 Å2 / ksol: 0.377374 e/Å3
Displacement parametersBiso mean: 13.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.45 Å20 Å20 Å2
2--1.45 Å20 Å2
3----2.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.5→24.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1405 0 43 210 1658
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_mcbond_it1.591.5
X-RAY DIFFRACTIONc_mcangle_it2.632
X-RAY DIFFRACTIONc_scbond_it2.52
X-RAY DIFFRACTIONc_scangle_it3.822.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.24 241 5.5 %
Rwork0.221 4130 -
obs--87.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water.paramwater.top
X-RAY DIFFRACTION4bb2.parambb2.top

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