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- PDB-1lru: Crystal Structure of E.coli Peptide Deformylase Complexed with An... -

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Basic information

Entry
Database: PDB / ID: 1lru
TitleCrystal Structure of E.coli Peptide Deformylase Complexed with Antibiotic Actinonin
ComponentsPEPTIDE DEFORMYLASE
KeywordsHYDROLASE / ACTINONIN / INHIBITION / POLYPEPTIDE DEFORMYLASE
Function / homology
Function and homology information


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
ACTINONIN / Peptide deformylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.1 Å
AuthorsGuilloteau, J.-P. / Mathieu, M. / Giglione, C. / Blanc, V. / Dupuy, A. / Chevrier, M. / Gil, P. / Famechon, A. / Meinnel, T. / Mikol, V.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: The crystal structures of four peptide deformylases bound to the antibiotic actinonin reveal two distinct types: a platform for the structure-based design of antibacterial agents.
Authors: Guilloteau, J.P. / Mathieu, M. / Giglione, C. / Blanc, V. / Dupuy, A. / Chevrier, M. / Gil, P. / Famechon, A. / Meinnel, T. / Mikol, V.
History
DepositionMay 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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

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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)59,22411
Polymers57,6793
Non-polymers1,5458
Water8,755486
1
A: PEPTIDE DEFORMYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6773
Polymers19,2261
Non-polymers4512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PEPTIDE DEFORMYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8695
Polymers19,2261
Non-polymers6434
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PEPTIDE DEFORMYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6773
Polymers19,2261
Non-polymers4512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: PEPTIDE DEFORMYLASE
hetero molecules

C: PEPTIDE DEFORMYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5468
Polymers38,4522
Non-polymers1,0946
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area3370 Å2
ΔGint-108 kcal/mol
Surface area16190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.040, 63.608, 83.494
Angle α, β, γ (deg.)90.00, 123.35, 90.00
Int Tables number5
Space group name H-MC121
Detailsthe biological unit is the monomer. There are three monomers in the asymetric unit.

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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) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6K3, peptide deformylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: 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.: 3 / Source method: obtained synthetically / Formula: C19H35N3O5 / Comment: antibiotic*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / 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: 2.6 Å3/Da / Density % sol: 54.63 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.5M (NH4)2SO4, 28%PEG400, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 19 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 mMMES-NaOH1droppH6.0
21.0 Mammonium sulfate1drop
30.5 mMprotein1drop
40.5 mMactinonin1drop
550 mMMES-NaOH1reservoirpH6.0
62.0 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 Å
DetectorType: MAC Science DIP-2000 / Detector: IMAGE PLATE / Date: Apr 14, 1997
RadiationMonochromator: Ni MIRROR + Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→15 Å / Num. all: 34394 / Num. obs: 34394 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rsym value: 0.076
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 2.3 % / Num. unique all: 3037 / Rsym value: 0.251 / % possible all: 83.7
Reflection
*PLUS
Lowest resolution: 15 Å / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
Highest resolution: 2.1 Å / % possible obs: 83.7 % / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 5

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Processing

Software
NameClassification
SHARPphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.1→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection
Rwork0.24 -
all0.24 34376
obs0.24 34376
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3879 0 94 486 4459
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg1.8
Refinement
*PLUS
Highest resolution: 2.1 Å / Rfactor obs: 0.24 / Rfactor Rwork: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS

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