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- PDB-1lqw: Crystal Structure of S.aureus Peptide Deformylase -

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Basic information

Entry
Database: PDB / ID: 1lqw
TitleCrystal Structure of S.aureus Peptide Deformylase
ComponentsPEPTIDE DEFORMYLASE PDF1
KeywordsHYDROLASE / PDF / PEPTIDE DEFORMYLASE
Function / homology
Function and homology information


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
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsMikol, 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 14, 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

Downloads & links

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Assembly

Deposited unit
A: PEPTIDE DEFORMYLASE PDF1
B: PEPTIDE DEFORMYLASE PDF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3084
Polymers41,1772
Non-polymers1312
Water3,153175
1
A: PEPTIDE DEFORMYLASE PDF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6542
Polymers20,5891
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PEPTIDE DEFORMYLASE PDF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6542
Polymers20,5891
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.210, 42.190, 101.670
Angle α, β, γ (deg.)90.00, 98.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PEPTIDE DEFORMYLASE PDF1


Mass: 20588.576 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P68826, peptide deformylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 50.43 %
Crystal growTemperature: 299 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 2.08M K2HPO4/NAH2PO4, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 299K
Crystal grow
*PLUS
Temperature: 19 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.04 Msodium potassium phosphate1droppH4.8
20.65 mMprotein1drop
32.08 Msodium potassium phosphate1reservoirpH4.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.933 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 9, 1999
RadiationMonochromator: SYNCHROTRON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.87→26 Å / Num. all: 33121 / Num. obs: 33121 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 29.5 Å2 / Rsym value: 0.046 / Net I/σ(I): 9.8
Reflection shellResolution: 1.87→1.97 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 4647 / Rsym value: 0.274 / % possible all: 95.4
Reflection
*PLUS
Rmerge(I) obs: 0.046
Reflection shell
*PLUS
% possible obs: 95.4 % / Rmerge(I) obs: 0.274

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR98.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→26 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1656 5 %RANDOM
Rwork0.231 ---
all0.231 32301 --
obs0.231 32301 --
Refinement stepCycle: LAST / Resolution: 1.87→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2875 0 2 175 3052
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg1.65
Refinement
*PLUS
Lowest resolution: 100 Å / Num. reflection obs: 30645 / % reflection Rfree: 5 % / Rfactor obs: 0.231 / Rfactor Rfree: 0.265 / Rfactor Rwork: 0.231
Solvent computation
*PLUS
Displacement parameters
*PLUS

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