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- PDB-2ai8: E.coli Polypeptide Deformylase complexed with SB-485343 -

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Basic information

Entry
Database: PDB / ID: 2ai8
TitleE.coli Polypeptide Deformylase complexed with SB-485343
ComponentsPeptide deformylase
KeywordsHYDROLASE
Function / homology
Function and homology information


co-translational protein modification / peptide deformylase / peptide deformylase activity / ferrous iron binding / ribosome binding / hydrolase activity / translation / zinc ion binding / cytosol
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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 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_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_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,3999
Polymers57,6793
Non-polymers7206
Water8,863492
1
A: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4663
Polymers19,2261
Non-polymers2402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4663
Polymers19,2261
Non-polymers2402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4663
Polymers19,2261
Non-polymers2402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.178, 63.350, 85.672
Angle α, β, γ (deg.)90.00, 121.23, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Peptide deformylase / PDF / Polypeptide deformylase


Mass: 19226.248 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: def, fms / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6K3, peptide deformylase
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-SB7 / [HYDROXY(3-PHENYLPROPYL)AMINO]METHANOL / SB-485345


Mass: 181.232 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 492 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.6 %

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 68611 / Num. obs: 68611 / % possible obs: 97.7 % / Redundancy: 2.3 % / Rsym value: 0.052 / Net I/σ(I): 20.3
Reflection shellResolution: 1.7→1.72 Å / Redundancy: 4.6 % / Rsym value: 0.172 / % possible all: 96.6

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT1.7data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→20 Å / σ(F): 367
RfactorNum. reflection% reflection
Rfree0.226 3476 5 %
Rwork0.212 --
all-68612 -
obs-68177 97.2 %
Solvent computationBsol: 38.445 Å2
Displacement parametersBiso mean: 14.856 Å2
Baniso -1Baniso -2Baniso -3
1-1.949 Å20 Å2-0.828 Å2
2---0.123 Å20 Å2
3----1.826 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3979 0 42 492 4513
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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