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- PDB-1rl4: Plasmodium falciparum peptide deformylase complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 1rl4
TitlePlasmodium falciparum peptide deformylase complex with inhibitor
Componentsformylmethionine deformylase
KeywordsHYDROLASE / crystal engineering / drug design / malaria / PDF / peptide deformylase / Plasmodium
Function / homology
Function and homology information


apicoplast / co-translational protein modification / N-terminal protein amino acid modification / peptide deformylase / peptide deformylase activity / ferrous iron binding / translation / mitochondrion / membrane
Similarity search - Function
Peptide Deformylase / Peptide deformylase / Peptide deformylase / Peptide deformylase superfamily / Polypeptide deformylase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-BL5 / Chem-BRR / : / Peptide deformylase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsRobien, M.A. / Nguyen, K.T. / Kumar, A. / Hirsh, I. / Turley, S. / Pei, D. / Hol, W.G.J.
Citation
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.J.
#1: 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.J.
History
DepositionNov 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 23, 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_ncs_dom_lim / 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.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_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_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
Remark 600HETEROGEN AS DISCUSSED IN REFERENCE 1 (ROBIEN ET AL, PROTEIN SCIENCE), THE MODEL CHOSEN FOR BL5, ...HETEROGEN AS DISCUSSED IN REFERENCE 1 (ROBIEN ET AL, PROTEIN SCIENCE), THE MODEL CHOSEN FOR BL5, PARTICULARLY IN THE ATOMS LINKING THE TWO HALVES OF THIS MOLECULE, WAS CHOSEN BASED ON THE ELECTRON DENSITY FEATURE USING OMIT MAPS. FROM THE PROTEIN SCIENCE MANUSCRIPT: ALTHOUGH THE IDENTITY OF THE LINKER ATOMS ARE UNKNOWN, A LINEAR -CH2-NH-NH-CH2- CHAIN IS APPROXIMATELY THE CORRECT SIZE. BECAUSE OF THE UNCERTAINTY PERTAINING TO THE LINKER, THE MODEL CHOSEN FOR THE LINKER SHOULD BE CONSIDERED AS EXPLORATORY AND PROVISIONAL, RATHER THAN CONCLUSIVE. WATERS 701-753 AND 801-818, CO 301, BRR 401, AND BL5 501 ARE ASSOCIATED WITH CHAIN A. WATERS 1701-1753 AND 901-953, CO 1301, BRR 1401, AND BL5 1501 ARE ASSOCIATED WITH CHAIN B.
Remark 999SEQUENCE THE NUMBERING OF RESIDUES IS BASED ON THE FULL SEQUENCE OF THE P.FALCIPARUM PDF PROTEIN, ...SEQUENCE THE NUMBERING OF RESIDUES IS BASED ON THE FULL SEQUENCE OF THE P.FALCIPARUM PDF PROTEIN, WHICH HAS A LARGE N-TERMINAL (APICOPLAST TARGETING) SIGNAL SEQUENCE, WHICH IS TRUNCATED IN VIVO IN THE PROCESS OF TRANSPORT INTO THE APICOPLAST ORGANELLE. A CONSTRUCT WITH AN N-TERMINAL 57 RESIDUE TRUNCATION WAS EXPRESSED IN E COLI FOR THIS STUDY. THE C-TERMINAL SEQUENCE USED IN THIS STUDY DIFFERS FROM THAT USED FOR PDB ENTRY 1JYM BY THE DELETION OF THREE RESIDUES (-EEP-) JUST PRIOR TO THE -LEHHHHHH OF THE HEXAHISTADINE TAG. THIS MODIFICATION WAS UNDERTAKEN AS A SUCCESSFUL EFFORT OF CRYSTAL ENGINEERING TO AVOID A NETWORK OF UNDESIRABLE CRYSTAL CONTACTS IN THE PREVIOUS STUDY. THE SEQUENCE OF P. FALCIPARUM PDF IN THIS DEPOSITION INCLUDES TWO SINGLE AMINO ACID CORRECTIONS TO THE SEQUENCE REPORTED IN THE ORIGINAL DEPOSITION (1JYM) OF P. FALCIPARUM PDF. RESIDUES GLU81 AND PRO160 HAD BEEN INADVERTENTLY NOT INCLUDED IN THE SEQUENCE USED DURING THE TRACING OF THE ELECTRON DENSITY OF THE ORIGINAL STUDY. THE RESIDUE NUMBERING OF THIS DEPOSITION REFLECTS THE MODIFIED, CORRECTED SEQUENCE INFORMATION, AND NOW AGREES WITH THE SEQUENCE DATA DERIVED FROM THE DEPOSITED P. FALCIPARUM GENOME.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: formylmethionine deformylase
B: formylmethionine deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4308
Polymers44,5442
Non-polymers1,8866
Water2,504139
1
A: formylmethionine deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2154
Polymers22,2721
Non-polymers9433
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: formylmethionine deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2154
Polymers22,2721
Non-polymers9433
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.317, 102.317, 118.339
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B
151A
161B
171A
181B
191A
201B
211A
221B
231A
241B
251A
261B
271A
281A
291A
301A
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ILEILEASPASP5AA67 - 7211 - 16
211ILEILEASPASP5BB67 - 7211 - 16
321PROPROVALVAL2AA73 - 12117 - 65
421PROPROVALVAL2BB73 - 12117 - 65
531ILEILESERSER2AA136 - 14680 - 90
631ILEILESERSER2BB136 - 14680 - 90
741LEULEULEULEU4AA14791
841LEULEULEULEU4BB14791
951VALVALCYSCYS2AA148 - 15692 - 100
1051VALVALCYSCYS2BB148 - 15692 - 100
1161LEULEULEULEU6AA157101
1261LEULEULEULEU6BB157101
1371SERSERPHEPHE2AA158 - 159102 - 103
1471SERSERPHEPHE2BB158 - 159102 - 103
1581PROPROILEILE4AA160 - 162104 - 106
1681PROPROILEILE4BB160 - 162104 - 106
1791GLUGLUGLUGLU2AA163 - 167107 - 111
1891GLUGLUGLUGLU2BB163 - 167107 - 111
19101ARGARGARGARG5AA168112
20101ARGARGARGARG5BB168112
21111PROPROILEILE2AA169 - 171113 - 115
22111PROPROILEILE2BB169 - 171113 - 115
23121VALVALILEILE6AA172 - 174116 - 118
24121VALVALILEILE6BB172 - 174116 - 118
25131SERSERLYSLYS2AA175 - 211119 - 155
26131SERSERLYSLYS2BB175 - 211119 - 155
27141COCOBL5BL52AC - E301 - 501
28141COCOBL5BL52A - BC - H301 - 1501
29151HOHHOHHOHHOH4AI701 - 753
30151HOHHOHHOHHOH4A - BI - J701 - 1753
112METMETASPASP5AA212 - 230156 - 174
212METMETLYSLYS5BB212 - 232156 - 176

NCS ensembles :
ID
1
2

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Components

#1: Protein formylmethionine deformylase /


Mass: 22271.871 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / 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.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-BRR / (2R)-2-{[FORMYL(HYDROXY)AMINO]METHYL}HEXANOIC ACID


Mass: 189.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO4
#4: Chemical ChemComp-BL5 / 2-{N'-[2-(5-AMINO-1-PHENYLCARBAMOYL-PENTYLCARBAMOYL)-HEXYL]-HYDRAZINOMETHYL}-HEXANOIC ACID(5-AMINO-1-PHENYLCARBAMOYL-PENTYL)-AMIDE


Mass: 694.950 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C38H62N8O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 4.01 Å3/Da / Density % sol: 69.35 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: sodium monobasic phosphate, potassium dibasic phosphate, lithium sulfate, CAPS, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMHEPES1droppH6.0
210 mM1dropNaCl
36.8 mg/mlprotein1drop
41.2 M1reservoirNaH2PO4
50.8 M1reservoirK2HPO4
60.2 M1reservoirLi2SO4
70.1 MCAPS1reservoirpH6.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 17, 2002
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.18→41.6 Å / Num. obs: 36742 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 33.9 Å2 / Rsym value: 0.111 / Net I/σ(I): 11.4
Reflection shellResolution: 2.18→2.3 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 5325 / Rsym value: 0.714 / % possible all: 100
Reflection
*PLUS
Num. measured all: 230882 / Rmerge(I) obs: 0.111
Reflection shell
*PLUS
Lowest resolution: 2.24 Å / Rmerge(I) obs: 0.714

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JYM

1jym


Resolution: 2.18→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.829 / SU ML: 0.073 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.134
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.2122 1811 4.9 %RANDOM
Rwork0.1973 ---
all0.19806 36594 --
obs0.19806 36594 99.99 %-
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: 39.587 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.18→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2555 0 128 139 2822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222728
X-RAY DIFFRACTIONr_angle_refined_deg1.3132.0023643
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8725306
X-RAY DIFFRACTIONr_chiral_restr0.0960.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021966
X-RAY DIFFRACTIONr_nbd_refined0.230.31279
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.5134
X-RAY DIFFRACTIONr_metal_ion_refined0.0140.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.334
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3040.514
X-RAY DIFFRACTIONr_mcbond_it2.44241556
X-RAY DIFFRACTIONr_mcangle_it4.31482539
X-RAY DIFFRACTIONr_scbond_it5.72781172
X-RAY DIFFRACTIONr_scangle_it8.397121104
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1466tight positional0.040.05
1655medium positional0.270.5
276medium positional0.470.5
163loose positional0.445
284loose positional1.35
1466tight thermal0.451
1655medium thermal1.443
276medium thermal1.183
163loose thermal3.0510
284loose thermal5.5610
LS refinement shellResolution: 2.18→2.236 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.272 122
Rwork0.251 2550
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.214 / Rfactor Rwork: 0.198
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_deg1.315
X-RAY DIFFRACTIONr_chiral_restr0.098
LS refinement shell
*PLUS
Highest resolution: 2.18 Å / Lowest resolution: 2.24 Å / Rfactor Rfree: 0.275

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