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- PDB-3e3u: Crystal structure of Mycobacterium tuberculosis peptide deformyla... -

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Basic information

Entry
Database: PDB / ID: 3e3u
TitleCrystal structure of Mycobacterium tuberculosis peptide deformylase in complex with inhibitor
ComponentsPeptide deformylase
KeywordsHYDROLASE / metallo-enzyme / Iron / Metal-binding / Protein biosynthesis
Function / homology
Function and homology information


protein deacylation / co-translational protein modification / N-terminal protein amino acid modification / peptidyl-methionine modification / 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 / Chem-NVC / Peptide deformylase / Peptide deformylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.56 Å
AuthorsMeng, W. / Xu, M. / Pan, S. / Koehn, J.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2008
Title: Peptide deformylase inhibitors of Mycobacterium tuberculosis: synthesis, structural investigations, and biological results.
Authors: Pichota, A. / Duraiswamy, J. / Yin, Z. / Keller, T.H. / Alam, J. / Liung, S. / Lee, G. / Ding, M. / Wang, G. / Chan, W.L. / Schreiber, M. / Ma, I. / Beer, D. / Ngew, X. / Mukherjee, K. / ...Authors: Pichota, A. / Duraiswamy, J. / Yin, Z. / Keller, T.H. / Alam, J. / Liung, S. / Lee, G. / Ding, M. / Wang, G. / Chan, W.L. / Schreiber, M. / Ma, I. / Beer, D. / Ngew, X. / Mukherjee, K. / Nanjundappa, M. / Teo, J.W. / Thayalan, P. / Yap, A. / Dick, T. / Meng, W. / Xu, M. / Koehn, J. / Pan, S.H. / Clark, K. / Xie, X. / Shoen, C. / Cynamon, M.
History
DepositionAug 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)22,0975
Polymers20,9601
Non-polymers1,1374
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.870, 54.765, 40.215
Angle α, β, γ (deg.)90.00, 94.39, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Peptide deformylase / PDF / Polypeptide deformylase


Mass: 20959.689 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: def / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P96275, UniProt: P9WIJ3*PLUS, 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-NVC / N-[(2R)-2-{[(2S)-2-(1,3-benzoxazol-2-yl)pyrrolidin-1-yl]carbonyl}hexyl]-N-hydroxyformamide


Mass: 359.420 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H25N3O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsBIOLOGICALLY RELAVENT BINDING MODE FOR INHIBITOR 16A IS THE BINDING OF RESIDUE NVC A201.

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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: 53.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.0 M Ammonium sulfate, Tris-HCl pH 7.5, 5mM Compound 16a, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 23, 2005 / Details: Multi-layer mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.56→50.32 Å / Num. all: 32726 / Num. obs: 32726 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 30.6
Reflection shellResolution: 1.56→1.62 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 2.9 / Num. unique all: 3027 / % possible all: 97.2

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
REFMACrefinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.56→50.32 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.418 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1567 5 %RANDOM
Rwork0.171 ---
all0.173 31159 --
obs0.173 31159 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61 Å2 / Biso mean: 18.589 Å2 / Biso min: 9.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å2-0.01 Å2
2--0.95 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.56→50.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1461 0 79 259 1799
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.795
X-RAY DIFFRACTIONc_bond_deg0.01
LS refinement shellResolution: 1.56→1.598 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.427 105 -
Rwork0.368 2042 -
all-2147 -
obs-2042 94 %

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