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- PDB-1g27: CRYSTAL STRUCTURE OF E.COLI POLYPEPTIDE DEFORMYLASE COMPLEXED WIT... -

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Basic information

Entry
Database: PDB / ID: 1g27
TitleCRYSTAL STRUCTURE OF E.COLI POLYPEPTIDE DEFORMYLASE COMPLEXED WITH THE INHIBITOR BB-3497
ComponentsPOLYPEPTIDE DEFORMYLASE
KeywordsHYDROLASE / BB-3497 / inhibition / Polypeptide deformylase
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
Chem-BB1 / NICKEL (II) ION / Peptide deformylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsClements, J.M. / Beckett, P. / Brown, A. / Catlin, C. / Lobell, M. / Palan, S. / Thomas, W. / Whittaker, M. / Baker, P.J. / Rodgers, H.F. ...Clements, J.M. / Beckett, P. / Brown, A. / Catlin, C. / Lobell, M. / Palan, S. / Thomas, W. / Whittaker, M. / Baker, P.J. / Rodgers, H.F. / Barynin, V. / Rice, D.W. / Hunter, M.G.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2001
Title: Antibiotic activity and characterization of BB-3497, a novel peptide deformylase inhibitor.
Authors: Clements, J.M. / Beckett, R.P. / Brown, A. / Catlin, G. / Lobell, M. / Palan, S. / Thomas, W. / Whittaker, M. / Wood, S. / Salama, S. / Baker, P.J. / Rodgers, H.F. / Barynin, V. / Rice, D.W. / Hunter, M.G.
History
DepositionOct 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 7, 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: POLYPEPTIDE DEFORMYLASE
B: POLYPEPTIDE DEFORMYLASE
C: POLYPEPTIDE DEFORMYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8439
Polymers57,6793
Non-polymers1,1646
Water1,36976
1
A: POLYPEPTIDE DEFORMYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6143
Polymers19,2261
Non-polymers3882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: POLYPEPTIDE DEFORMYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6143
Polymers19,2261
Non-polymers3882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: POLYPEPTIDE DEFORMYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6143
Polymers19,2261
Non-polymers3882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.140, 64.470, 85.290
Angle α, β, γ (deg.)90.00, 123.11, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

#1: Protein POLYPEPTIDE DEFORMYLASE / E.C.3.5.1.31 / N-FORMYLMETHIONYLAMINOACYL-TRNA DEFORMYLASE / PDF / FMS


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 / Plasmid: PET24-PDF / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P0A6K3, EC: 3.5.1.31
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-BB1 / 2-[(FORMYL-HYDROXY-AMINO)-METHYL]-HEXANOIC ACID (1-DIMETHYLCARBAMOYL-2,2-DIMETHYL-PROPYL)-AMIDE / BB-3497


Mass: 329.435 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H31N3O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.86 Å3/Da / Density % sol: 56.94 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 10mg/ml PDF, 20mM BB-3497, 25% PEG 4000, 0.1M sodium citrate, 0.2M ammonium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP at 290K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
220 mMinhibitor1drop
350 mMHEPES1drop
425-32 %PEG40001reservoir
50.1 Msodium citrate1reservoir
60.2 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Apr 20, 1999
RadiationMonochromator: MSC Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 38303 / Num. obs: 36273 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.95 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.2
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.24 / % possible all: 92.7
Reflection shell
*PLUS
Lowest resolution: 2.15 Å / % possible obs: 92.7 % / Num. unique obs: 2368 / Mean I/σ(I) obs: 3.9

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Processing

Software
NameVersionClassification
AMoREphasing
TNT5Erefinement
MAR345data collection
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1824 5.3 %random
Rwork0.21 ---
all0.21 34657 --
obs0.21 34657 --
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3945 0 72 76 4093
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg1.043
X-RAY DIFFRACTIONt_bond_d0.014
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.3 % / Rfactor obs: 0.21 / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS

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