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- PDB-2ai7: S.pneumoniae Polypeptide Deformylase complexed with SB-485345 -

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Basic information

Entry
Database: PDB / ID: 2ai7
TitleS.pneumoniae Polypeptide Deformylase complexed with SB-485345
ComponentsPeptide deformylase
KeywordsHYDROLASE
Function / homology
Function and homology information


co-translational protein 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 / [HYDROXY(3-PHENYLPROPYL)AMINO]METHANOL / Peptide deformylase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2 Å
AuthorsSmith, K.J. / Petit, C.M. / Aubart, K. / Smyth, M. / McManus, E. / Jones, J. / Fosberry, A. / Lewis, C. / Lonetto, M. / Christensen, S.B.
CitationJournal: Protein Sci. / Year: 2003
Title: Structural Variation and inhibitor binding in polypeptide deformylase from four different bacterial species
Authors: Smith, K.J. / Petit, C.M. / Aubart, K. / Smyth, M. / McManus, E. / Jones, J. / Fosberry, A. / Lewis, C. / Lonetto, M. / Christensen, S.B.
History
DepositionJul 29, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)23,0184
Polymers22,6821
Non-polymers3363
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.889, 49.889, 91.565
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: 22682.037 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: ATCC BAA-255 R6 / Gene: def / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DP79, 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.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-SB7 / [HYDROXY(3-PHENYLPROPYL)AMINO]METHANOL / SB-485345


Mass: 181.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 3.1 Å3/Da / Density % sol: 60.6 %

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Data collection

RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 17182 / Num. obs: 17182 / % possible obs: 98.6 % / Redundancy: 3.5 % / Rsym value: 0.056 / Net I/σ(I): 20.9
Reflection shellResolution: 2→2.05 Å / Mean I/σ(I) obs: 2.5 / Rsym value: 0.228 / % possible all: 98.3

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT1.7data extraction
RefinementMethod to determine structure: MAD / Resolution: 2→20 Å / Redundancy reflection obs: 15032 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.263 1521 10.1 %
Rwork0.22 --
all-15032 -
obs-15032 99.4 %
Solvent computationBsol: 66.726 Å2
Displacement parametersBiso mean: 29.697 Å2
Baniso -1Baniso -2Baniso -3
1--4.741 Å20 Å20 Å2
2---4.741 Å20 Å2
3---9.483 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1519 0 19 137 1675
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3CNS_TOPPAR:water.param
X-RAY DIFFRACTION4PEG_mod.param
X-RAY DIFFRACTION5sb4.par

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