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- PDB-1jym: Crystals of Peptide Deformylase from Plasmodium falciparum with T... -

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Basic information

Entry
Database: PDB / ID: 1jym
TitleCrystals of Peptide Deformylase from Plasmodium falciparum with Ten Subunits per Asymmetric Unit Reveal Critical Characteristics of the Active Site for Drug Design
ComponentsPeptide Deformylase
KeywordsHYDROLASE / PDF / malaria / plasmodium / deformylation / metalloenzyme
Function / homology
Function and homology information


N-terminal protein amino acid modification / apicoplast / peptide deformylase / peptide deformylase activity / : / ferrous iron binding / translation / membrane
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
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsKumar, A. / Nguyen, K.T. / Srivathsan, S. / Ornstein, B. / Turley, S. / Hirsh, I. / Pei, D. / Hol, W.G.J.
Citation
Journal: Structure / Year: 2002
Title: Crystals of peptide deformylase from Plasmodium falciparum reveal critical characteristics of the active site for drug design.
Authors: Kumar, A. / Nguyen, K.T. / Srivathsan, S. / Ornstein, B. / Turley, S. / Hirsh, I. / Pei, D. / Hol, W.G.
#1: Journal: Protein Sci. / Year: 2004
Title: An improved crystal form of Plasmodium falciparum peptide deformylase
Authors: Robien, M.A. / Nguyen, K.T. / Kumar, A. / Hirsh, I. / Turley, S. / Pei, D. / Hol, W.G.
History
DepositionSep 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2002Provider: repository / Type: Initial release
Revision 1.1May 5, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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_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.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.pdbx_leaving_atom_flag / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptide Deformylase
B: Peptide Deformylase
C: Peptide Deformylase
D: Peptide Deformylase
E: Peptide Deformylase
F: Peptide Deformylase
G: Peptide Deformylase
H: Peptide Deformylase
I: Peptide Deformylase
J: Peptide Deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,80820
Polymers218,21810
Non-polymers58910
Water3,189177
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.263, 121.263, 177.272
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
Peptide Deformylase


Mass: 21821.820 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PDF / Plasmid: pET29b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8I372, EC: 3.5.1.31
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Tris, Sodium chloride, Magnesium chloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMcacodylate1droppH6.5
20.1 M1dropNaCl
320 mg/mlprotein1drop
40.1 MTris1reservoir
52.5 M1reservoirNaCl
60.2 M1reservoirpH7.0MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97918, 0.97938, 0.96396
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 5, 2001
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979181
20.979381
30.963961
ReflectionResolution: 2.8→30 Å / Num. all: 62948 / Num. obs: 51866 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rsym value: 0.101
Reflection shellResolution: 2.8→2.9 Å / Rsym value: 0.594 / % possible all: 97.1
Reflection
*PLUS
Num. obs: 62948 / Rmerge(I) obs: 0.101
Reflection shell
*PLUS
% possible obs: 97.1 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 4.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
REFMAC5refinement
RefinementMethod to determine structure: MAD
Starting model: PDB ENTRY 1DFF

1dff


Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.826 / SU B: 21.435 / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.489 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.29599 2632 5.1 %RANDOM
Rwork0.23062 ---
all0.23395 51866 --
obs0.2339 49234 82.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.586 Å2
Baniso -1Baniso -2Baniso -3
1--4.64 Å20 Å20 Å2
2---4.64 Å20 Å2
3---9.28 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14397 0 20 167 14584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02214703
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6861.96619668
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.77531726
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.593153088
X-RAY DIFFRACTIONr_chiral_restr0.1360.22168
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210700
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.37099
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.51017
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.3159
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2760.514
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it3.29748663
X-RAY DIFFRACTIONr_mcangle_it5.644814146
X-RAY DIFFRACTIONr_scbond_it5.84786040
X-RAY DIFFRACTIONr_scangle_it8.416125522
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.9 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.338 119
Rwork0.272 2200
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 5.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.7
LS refinement shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / Rfactor Rwork: 0.272

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