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- PDB-4e9a: Structure of Peptide Deformylase form Helicobacter Pylori in comp... -

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Basic information

Entry
Database: PDB / ID: 4e9a
TitleStructure of Peptide Deformylase form Helicobacter Pylori in complex with inhibitor
ComponentsPeptide deformylase 11
KeywordsHYDROLASE
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
: / Chem-QAP / Peptide deformylase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.662 Å
AuthorsCui, K. / Zhu, L. / Lu, W. / Huang, J.
CitationJournal: To be Published
Title: Identification of Novel Peptide Deformylase Inhibitors from Natural Products
Authors: Cui, K. / Zhu, L. / Lu, W. / Huang, J.
History
DepositionMar 20, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7466
Polymers21,0081
Non-polymers7385
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.891, 52.057, 92.064
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Peptide deformylase 11 / PDF 11 / Polypeptide deformylase 11


Mass: 21008.465 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 2-164
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: def, def11 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q672W7, peptide deformylase

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Non-polymers , 5 types, 92 molecules

#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-QAP / 2-phenylethyl (2E)-3-(3,4-dihydroxyphenyl)prop-2-enoate


Mass: 284.307 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H16O4
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.39 Å3/Da / Density % sol: 48.52 %
Crystal growTemperature: 290 K / Method: evaporation / pH: 7.5 / Details: HEPES, MPD, pH 7.5, EVAPORATION, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.66→34.484 Å / Num. obs: 24141

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EW7

2ew7


Resolution: 1.662→34.48 Å / SU ML: 0.16 / σ(F): 1.35 / Phase error: 19.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2302 1229 5.09 %
Rwork0.2076 --
obs0.2088 24141 98.84 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.855 Å2 / ksol: 0.377 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å2-0 Å2
2--0.3879 Å2-0 Å2
3---0.0921 Å2
Refinement stepCycle: LAST / Resolution: 1.662→34.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1308 0 45 87 1440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071372
X-RAY DIFFRACTIONf_angle_d1.0981841
X-RAY DIFFRACTIONf_dihedral_angle_d18536
X-RAY DIFFRACTIONf_chiral_restr0.073205
X-RAY DIFFRACTIONf_plane_restr0.004229
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6616-1.72820.2681120.2692245897
1.7282-1.80680.25021410.22972539100
1.8068-1.90210.21151500.19312515100
1.9021-2.02120.18821420.18272536100
2.0212-2.17730.21621460.17712533100
2.1773-2.39630.2071180.1932576100
2.3963-2.74290.22661430.19572577100
2.7429-3.45530.21131240.1991259899
3.4553-34.49130.25461530.228258095

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