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- PDB-3m6o: Crystal structure of Arabidopsis thaliana peptide deformylase 1B ... -

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Basic information

Entry
Database: PDB / ID: 3m6o
TitleCrystal structure of Arabidopsis thaliana peptide deformylase 1B (AtPDF1B)
ComponentsPeptide deformylase 1B
KeywordsHYDROLASE / peptide deformylase / 1B / PDF / N-terminal excision pathway / NME / Arabidopsis thaliana / induced-fit / Metal-binding / Mitochondrion / Protein biosynthesis / Transit peptide
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
Peptide deformylase 1B, chloroplastic/mitochondrial
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_asym_id / _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 1B
B: Peptide deformylase 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,67213
Polymers43,9522
Non-polymers71911
Water8,899494
1
A: Peptide deformylase 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3697
Polymers21,9761
Non-polymers3926
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptide deformylase 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3036
Polymers21,9761
Non-polymers3275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.970, 55.940, 148.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 21976.232 Da / Num. of mol.: 2 / Fragment: residues 1-193
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 494 / 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: 2.65 Å3/Da / Density % sol: 53.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 17% PEG-3350, 0.2M zinc acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 16, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 32769 / Num. obs: 32457 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Rsym value: 0.094 / Net I/σ(I): 14.48
Reflection shellResolution: 1.99→2.11 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 5.1 / Rsym value: 0.455 / % possible all: 97.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RL4

1rl4


Resolution: 2→27.97 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.89 / SU B: 9.446 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28377 1637 5.1 %RANDOM
Rwork0.21703 ---
obs0.22052 30521 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.745 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å20 Å2
2--0.99 Å20 Å2
3----1.72 Å2
Refinement stepCycle: LAST / Resolution: 2→27.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2830 0 11 494 3335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222886
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0361.9933907
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1095358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.42924.815135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.44815508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6231518
X-RAY DIFFRACTIONr_chiral_restr0.1410.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022196
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2440.21549
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.21988
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2560.2305
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2250.212
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.390.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4190.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3671.51863
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7722914
X-RAY DIFFRACTIONr_scbond_it2.89731148
X-RAY DIFFRACTIONr_scangle_it4.0064.5993
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 101 -
Rwork0.261 2225 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1410.13970.180.5610.01220.7361-0.0228-0.05070.00930.0212-0.0595-0.00810.0078-0.22280.0823-0.0678-0.00040.00230.0444-0.0224-0.018212.889913.024431.9213
20.5932-0.03510.02730.48080.28280.8673-0.04650.0240.0105-0.0743-0.0212-0.0132-0.25390.00790.06770.03350.0006-0.0207-0.05890.0037-0.018428.807929.22375.2976
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 180
2X-RAY DIFFRACTION2B1 - 180

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