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- PDB-3m6q: Crystal structure of Arabidopsis thaliana peptide deformylase 1B ... -

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Basic information

Entry
Database: PDB / ID: 3m6q
TitleCrystal structure of Arabidopsis thaliana peptide deformylase 1B (AtPDF1B) G41Q mutant in complex with actinonin
ComponentsPeptide deformylase 1B
KeywordsHYDROLASE/ANTIBIOTIC / peptide deformylase / 1B / PDF / N-terminal excision pathway / NME / Arabidopsis thaliana / induced-fit / Hydrolase / Metal-binding / Mitochondrion / Protein biosynthesis / Transit peptide / HYDROLASE-ANTIBIOTIC complex
Function / homology
Function and homology information


peptide deformylase / peptide deformylase activity / chloroplast stroma / plastid / 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
ACTINONIN / Peptide deformylase 1B, chloroplastic/mitochondrial
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / rigid body / Resolution: 2.4 Å
AuthorsFieulaine, S. / Meinnel, T. / Giglione, C.
CitationJournal: Plos Biol. / Year: 2011
Title: Trapping conformational states along ligand-binding dynamics of peptide deformylase: the impact of induced fit on enzyme catalysis
Authors: Fieulaine, S. / Boularot, A. / Artaud, I. / Desmadril, M. / Dardel, F. / Meinnel, T. / Giglione, C.
History
DepositionMar 16, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Nov 1, 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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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

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Assembly

Deposited unit
A: Peptide deformylase 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7607
Polymers22,0471
Non-polymers7136
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.63, 56.63, 146.55
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Peptide deformylase 1B / PDF 1B / AtPDF1B / AtDEF2 / Polypeptide deformylase


Mass: 22047.311 Da / Num. of mol.: 1 / Fragment: residues 1-193 / Mutation: G41Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: def / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): Jm101Tr / References: UniProt: Q9FUZ2, peptide deformylase
#2: 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.: 1 / Source method: obtained synthetically / Formula: C19H35N3O5 / Comment: antitumor, antibiotic*YM
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.66 Å3/Da / Density % sol: 53.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% PEG-3350, 0.1M zinc acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 23, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 10385 / Num. obs: 10258 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12.9 % / Rsym value: 0.087 / Net I/σ(I): 22.77
Reflection shellResolution: 2.4→2.51 Å / Redundancy: 11.1 % / Mean I/σ(I) obs: 6.1 / Num. unique all: 1504 / Rsym value: 0.426 / % possible all: 93.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: rigid body
Starting model: PDB entry 3M6O

3m6o


Resolution: 2.4→45 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.3085 515 -RANDOM
Rwork0.2287 ---
all0.2327 ---
obs0.2327 9769 100 %-
Displacement parametersBiso mean: 36.8 Å2
Refinement stepCycle: LAST / Resolution: 2.4→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1409 0 32 148 1589
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.029
X-RAY DIFFRACTIONr_angle_refined_deg2.294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.06
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.883
LS refinement shellResolution: 2.4→2.429 Å
RfactorNum. reflection% reflection
Rfree0.28 35 -
Rwork0.277 --
obs--100 %

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