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- PDB-4je8: Crystal structure of a human-like mitochondrial peptide deformyla... -

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Basic information

Entry
Database: PDB / ID: 4je8
TitleCrystal structure of a human-like mitochondrial peptide deformylase in complex with Met-Ala-Ser
Components
  • Peptide deformylase 1A, chloroplastic/mitochondrial
  • tripeptide Met-Ala-Ser
KeywordsHYDROLASE/PEPTIDE / peptide deformylase / mitochondrial / HYDROLASE-PEPTIDE complex
Function / homology
Function and homology information


plant-type cell wall / co-translational protein modification / 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 / Resolution: 2.4 Å
AuthorsFieulaine, S. / Meinnel, T. / Giglione, C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Understanding the highly efficient catalysis of prokaryotic peptide deformylases by shedding light on the determinants specifying the low activity of the human counterpart.
Authors: Fieulaine, S. / Desmadril, M. / Meinnel, T. / Giglione, C.
History
DepositionFeb 26, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2014Group: Database references
Revision 1.2Nov 8, 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_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_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 1A, chloroplastic/mitochondrial
B: Peptide deformylase 1A, chloroplastic/mitochondrial
D: tripeptide Met-Ala-Ser
E: tripeptide Met-Ala-Ser
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4916
Polymers45,3604
Non-polymers1312
Water4,630257
1
A: Peptide deformylase 1A, chloroplastic/mitochondrial
D: tripeptide Met-Ala-Ser
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7463
Polymers22,6802
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-11 kcal/mol
Surface area10240 Å2
MethodPISA
2
B: Peptide deformylase 1A, chloroplastic/mitochondrial
E: tripeptide Met-Ala-Ser
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7463
Polymers22,6802
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-44 kcal/mol
Surface area9710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.550, 74.710, 109.760
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 1A, chloroplastic/mitochondrial / AtDEF1 / AtPDF1A / PDF 1A / Polypeptide deformylase


Mass: 22372.736 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 79-267 / Mutation: G47C, L112E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g15390, def, DEF1, F9L1.34, F9L1_34, PDF1A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FV53, peptide deformylase
#2: Protein/peptide tripeptide Met-Ala-Ser


Mass: 307.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemical product
#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.: 257 / 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: 2.33 Å3/Da / Density % sol: 47.21 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 5-15% PEG 5000 MME, 100mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2
DetectorDate: Apr 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 16326 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rsym value: 0.084 / Net I/σ(I): 11.68
Reflection shellResolution: 2.39→2.54 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 3.03 / Rsym value: 0.386 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
REFMAC5.2.0019phasing
RefinementStarting model: PDB entry 1ZXZ

1zxz


Resolution: 2.4→46.68 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.916 / SU B: 16.219 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.424 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: RIGID BODY HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25096 860 5 %RANDOM
Rwork0.17381 ---
obs0.17761 16326 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: 44.227 Å2
Baniso -1Baniso -2Baniso -3
1--2.15 Å20 Å20 Å2
2--4.83 Å20 Å2
3----2.68 Å2
Refinement stepCycle: LAST / Resolution: 2.4→46.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3005 0 2 257 3264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0223057
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.6671.9814138
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7655383
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.47524.043141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.8215534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5781526
X-RAY DIFFRACTIONr_chiral_restr0.1430.2469
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022312
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2290.21346
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.22009
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2188
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.3730.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2930.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2771.52017
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.79923106
X-RAY DIFFRACTIONr_scbond_it3.33731196
X-RAY DIFFRACTIONr_scangle_it4.8964.51032
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 63 -
Rwork0.229 1200 -
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)
12.2888-0.3654-0.11260.9030.28525.0861-0.0485-0.08250.12620.08430.02750.0151-0.063-0.60360.0211-0.32610.0106-0.017-0.01350.0883-0.19686.027-11.478-14.234
22.8434-0.4542-1.21991.18590.77555.57820.11410.4592-0.08290.00160.0952-0.34220.19030.2689-0.2093-0.3068-0.0101-0.00950.0019-0.0179-0.079225.685-20.745-40.493
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 193
2X-RAY DIFFRACTION2B3 - 191

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