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- PDB-5jmp: Structure of Plasmodium falciparum DXR in complex with a beta-sub... -

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Basic information

Entry
Database: PDB / ID: 5jmp
TitleStructure of Plasmodium falciparum DXR in complex with a beta-substituted fosmidomycin analogue, LC57 and manganese
Components1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic
KeywordsOXIDOREDUCTASE / ENZYME-INHIBITOR COMPLEX / MEP PATHWAY / ISOPRENOID BIOSYNTHESIS
Function / homology
Function and homology information


apicoplast / 1-deoxy-D-xylulose-5-phosphate reductoisomerase / 1-deoxy-D-xylulose-5-phosphate reductoisomerase activity / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / NADPH binding / metal ion binding
Similarity search - Function
1-deoxy-D-xylulose 5-phosphate reductoisomerase / 1-deoxy-D-xylulose 5-phosphate reductoisomerase, N-terminal / 1-deoxy-D-xylulose 5-phosphate reductoisomerase, C-terminal / DXP reductoisomerase C-terminal domain / DXP reductoisomerase, C-terminal domain superfamily / 1-deoxy-D-xylulose 5-phosphate reductoisomerase / 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal domain / DXP reductoisomerase C-terminal domain / RNA polymerase sigma factor, region 2, helix turn helix motif / Rna Polymerase Sigma Factor; Chain: A ...1-deoxy-D-xylulose 5-phosphate reductoisomerase / 1-deoxy-D-xylulose 5-phosphate reductoisomerase, N-terminal / 1-deoxy-D-xylulose 5-phosphate reductoisomerase, C-terminal / DXP reductoisomerase C-terminal domain / DXP reductoisomerase, C-terminal domain superfamily / 1-deoxy-D-xylulose 5-phosphate reductoisomerase / 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal domain / DXP reductoisomerase C-terminal domain / RNA polymerase sigma factor, region 2, helix turn helix motif / Rna Polymerase Sigma Factor; Chain: A / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
4-ethylmorpholine / Chem-LC7 / : / 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSooriyaarachchi, S. / Bergfors, T. / Jones, T.A. / Mowbray, S.L.
Funding support Sweden, 2items
OrganizationGrant numberCountry
FORMAS Sweden
VR Sweden
Citation
Journal: Chemmedchem / Year: 2016
Title: Targeting an Aromatic Hotspot in Plasmodium falciparum 1-Deoxy-d-xylulose-5-phosphate Reductoisomerase with beta-Arylpropyl Analogues of Fosmidomycin.
Authors: Sooriyaarachchi, S. / Chofor, R. / Risseeuw, M.D. / Bergfors, T. / Pouyez, J. / Dowd, C.S. / Maes, L. / Wouters, J. / Jones, T.A. / Van Calenbergh, S. / Mowbray, S.L.
#1: Journal: J. Med. Chem. / Year: 2015
Title: Synthesis and bioactivity of beta-substituted fosmidomycin analogues targeting 1-deoxy-D-xylulose-5-phosphate reductoisomerase.
Authors: Chofor, R. / Sooriyaarachchi, S. / Risseeuw, M.D. / Bergfors, T. / Pouyez, J. / Johny, C. / Haymond, A. / Everaert, A. / Dowd, C.S. / Maes, L. / Coenye, T. / Alex, A. / Couch, R.D. / Jones, ...Authors: Chofor, R. / Sooriyaarachchi, S. / Risseeuw, M.D. / Bergfors, T. / Pouyez, J. / Johny, C. / Haymond, A. / Everaert, A. / Dowd, C.S. / Maes, L. / Coenye, T. / Alex, A. / Couch, R.D. / Jones, T.A. / Wouters, J. / Mowbray, S.L. / Van Calenbergh, S.
History
DepositionApr 29, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic
B: 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,45125
Polymers96,3292
Non-polymers2,12223
Water9,314517
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6900 Å2
ΔGint17 kcal/mol
Surface area32930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.718, 56.580, 85.660
Angle α, β, γ (deg.)104.13, 103.33, 100.12
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic / DXP reductoisomerase


Mass: 48164.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: DXR, PF14_0641 / Organ: APICOPLAST / Plasmid: PEXP-5-CT/TOPO / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43
References: UniProt: Q8IKG4, 1-deoxy-D-xylulose-5-phosphate reductoisomerase

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Non-polymers , 6 types, 540 molecules

#2: Chemical ChemComp-LC7 / [(2R)-5-(3-fluorophenyl)-2-{2-[hydroxy(methyl)amino]-2-oxoethyl}pentyl]phosphonic acid


Mass: 333.292 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H21FNO5P
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-6LB / 4-ethylmorpholine


Mass: 115.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 517 / 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: 2.38 Å3/Da / Density % sol: 48.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% W/V PEG 8000, 20% V/V ethylene glycol, 0.1 M MES/imidazole pH6.5 0.02M amino amino acid ( 0.2M sodium L-glutamate, 0.2M DL-alanine, 0.2M glycine, 0.2M DL-lysine HCL, 0.2M DL serine)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.7→41.37 Å / Num. obs: 95608 / % possible obs: 97.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 7.4
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.602 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
Omodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: LC51, 5JAZ

5jaz


Resolution: 1.7→35 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.572 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20824 4761 5 %RANDOM
Rwork0.17806 ---
obs0.17955 90831 97.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.914 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å2-0.47 Å20.06 Å2
2--0.56 Å2-1.3 Å2
3---0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.7→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6552 0 134 517 7203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0196897
X-RAY DIFFRACTIONr_bond_other_d0.0020.026744
X-RAY DIFFRACTIONr_angle_refined_deg1.2031.9529286
X-RAY DIFFRACTIONr_angle_other_deg0.8832.98215600
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5025844
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.62426.388299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.023151289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.54156
X-RAY DIFFRACTIONr_chiral_restr0.0730.21057
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027661
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021489
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0571.9223334
X-RAY DIFFRACTIONr_mcbond_other1.0541.9213333
X-RAY DIFFRACTIONr_mcangle_it1.8182.8744183
X-RAY DIFFRACTIONr_mcangle_other1.8182.8754184
X-RAY DIFFRACTIONr_scbond_it1.2992.1783563
X-RAY DIFFRACTIONr_scbond_other1.2982.1783563
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1843.1765101
X-RAY DIFFRACTIONr_long_range_B_refined4.46716.0247993
X-RAY DIFFRACTIONr_long_range_B_other4.30315.7877829
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 350 -
Rwork0.282 6620 -
obs--96.55 %

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