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- PDB-1zy1: X-ray structure of peptide deformylase from Arabidopsis thaliana ... -

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Basic information

Entry
Database: PDB / ID: 1zy1
TitleX-ray structure of peptide deformylase from Arabidopsis thaliana (AtPDF1A) in complex with Met-Ala-Ser
Components
  • Peptide deformylase, mitochondrial
  • tripeptide fragment
KeywordsHYDROLASE / peptide deformylase / PDF1A / eukaryote / higher plant / Arabidopsis thaliana / zinc ion
Function / homology
Function and homology information


plant-type cell wall / peptide deformylase / peptide deformylase activity / : / chloroplast stroma / chloroplast / translation / mitochondrion / 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
Peptide deformylase 1A, chloroplastic/mitochondrial
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / rigid body / Resolution: 3 Å
AuthorsFieulaine, S. / Juillan-Binard, C. / Serero, A. / Dardel, F. / Giglione, C. / Meinnel, T. / Ferrer, J.-L.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: The crystal structure of mitochondrial (Type 1A) peptide deformylase provides clear guidelines for the design of inhibitors specific for the bacterial forms
Authors: Fieulaine, S. / Juillan-Binard, C. / Serero, A. / Dardel, F. / Giglione, C. / Meinnel, T. / Ferrer, J.-L.
History
DepositionJun 9, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_asym_id / _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_asym_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_asym_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

Downloads & links

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Assembly

Deposited unit
A: Peptide deformylase, mitochondrial
B: Peptide deformylase, mitochondrial
D: tripeptide fragment
E: tripeptide fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3676
Polymers45,2364
Non-polymers1312
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-101 kcal/mol
Surface area17170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.6, 76.3, 109.3
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
DetailsDimer in the asymmetric unit, but it is unclear whether it is a biological dimer or not

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Components

#1: Protein Peptide deformylase, mitochondrial / E.C.3.5.1.88 / PDF / Polypeptide deformylase


Mass: 22310.689 Da / Num. of mol.: 2 / Fragment: mature protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PDF1A / Plasmid: pQE30 derivative / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9FV53, peptide deformylase
#2: Protein/peptide tripeptide fragment


Mass: 307.367 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.5 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 5000 MME, MES, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.978 Å
DetectorType: MARRESEARCH 176mm / Detector: CCD / Date: Apr 15, 2005
RadiationMonochromator: 2 silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 9219 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 17.9

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Processing

Software
NameClassification
XDSdata scaling
XDSdata reduction
CNSrefinement
CNSphasing
RefinementMethod to determine structure: rigid body
Starting model: 1ZXZ

1zxz


Resolution: 3→30 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 471 -RANDOM
Rwork0.226 ---
all-9104 --
obs-8852 97.2 %-
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2988 0 2 66 3056
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg1.849

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