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- PDB-3pn2: Crystal structure of Arabidopsis thaliana petide deformylase 1B (... -

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Basic information

Entry
Database: PDB / ID: 3pn2
TitleCrystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) (crystallized in PEG-550-MME)
ComponentsPeptide deformylase 1B, chloroplastic
KeywordsHYDROLASE / peptide deformylase / 1B / PDF / N-terminal excision pathway / NME / induced-fit
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
DepositionNov 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3697
Polymers21,9761
Non-polymers3926
Water4,522251
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Peptide deformylase 1B, chloroplastic
hetero molecules

A: Peptide deformylase 1B, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,73714
Polymers43,9522
Non-polymers78512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area2420 Å2
ΔGint-394 kcal/mol
Surface area17400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.320, 56.320, 148.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 21976.232 Da / Num. of mol.: 1 / Fragment: UNP residues 83-273
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DEF2, PDF1B / 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.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.68 Å3/Da / Density % sol: 54.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% PEG-550-MME, Zinc sulfate 75mM, 70mM MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2008
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. obs: 15978 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Rsym value: 0.05 / Net I/σ(I): 12.6
Reflection shellResolution: 2→2.12 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.65 / Num. unique all: 4882 / Rsym value: 0.409 / % possible all: 98.9

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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 3M6O

3m6o


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.927 / SU B: 11.985 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25751 841 5 %RANDOM
Rwork0.20256 ---
obs0.20525 15978 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.124 Å2
Baniso -1Baniso -2Baniso -3
1-1.77 Å20 Å20 Å2
2--1.77 Å20 Å2
3----3.54 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1402 0 6 251 1659
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0221430
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8791.9891940
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1195179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.8624.77667
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.51915242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.567159
X-RAY DIFFRACTIONr_chiral_restr0.1310.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021096
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2250.2675
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.2984
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.250.2136
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1610.28
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.3070.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0691.5932
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.52121454
X-RAY DIFFRACTIONr_scbond_it2.8623562
X-RAY DIFFRACTIONr_scangle_it4.164.5486
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 59 -
Rwork0.246 1136 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -0.4386 Å / Origin y: 15.3112 Å / Origin z: 60.6058 Å
111213212223313233
T-0.2646 Å2-0.0228 Å2-0.0161 Å2-0.1828 Å2-0.0828 Å2---0.1302 Å2
L1.2425 °20.2396 °2-0.6115 °2-2.0382 °2-0.3757 °2--4.1295 °2
S0.0609 Å °0.1539 Å °0.0232 Å °-0.0908 Å °-0.2135 Å °0.1644 Å °0.0399 Å °-1.1212 Å °0.1525 Å °

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