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

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Basic information

Entry
Database: PDB / ID: 5jbi
TitleStructure of Plasmodium falciparum DXR in complex with a beta-substituted fosmidomycin analogue, LC52 and manganese
Components1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic
KeywordsOXIDOREDUCTASE / ENZYME-INHIBITOR COMPLEX / MEP PATHWAY / ISOPRENOID BIOSYNTHESIS
Function / homology
Function and homology information


isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway involved in terpenoid biosynthetic process / 1-deoxy-D-xylulose-5-phosphate reductoisomerase / 1-deoxy-D-xylulose-5-phosphate reductoisomerase activity / apicoplast / NADPH binding / manganese 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
Chem-6J8 / : / 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / 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 13, 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_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)98,15322
Polymers96,3292
Non-polymers1,82420
Water8,251458
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint25 kcal/mol
Surface area32620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.657, 56.397, 85.919
Angle α, β, γ (deg.)103.60, 102.96, 100.46
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 / Fragment: UNP residues 75-488
Source method: isolated from a genetically manipulated source
Details: MATURE PROTEIN LACKS SIGNAL AND APICOPLAST TARGETING SEQUENCES
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Gene: DXR, PF14_0641 / Organ: apicoplast / Plasmid: pEXP5-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 , 5 types, 478 molecules

#2: Chemical ChemComp-6J8 / [(2R)-2-{2-[hydroxy(methyl)amino]-2-oxoethyl}-5-(4-methoxyphenyl)pentyl]phosphonic acid


Mass: 345.328 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24NO6P
#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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 458 / 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: 2.42 Å3/Da / Density % sol: 49.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% PEG 8000, 20%ethylene glycol 0.1M MES/imidazole, pH 6.5 0.02M each alcohol: 1,6-hexanediol 1-butanol (RS)-1,2-propanediol 2-propanol 1,4-butanediol 1,3-propanediol

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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→48.78 Å / Num. obs: 95833 / % possible obs: 97.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 18.5 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 7.9
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.762 / Mean I/σ(I) obs: 1.8 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
Omodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5JAZ

5jaz


Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.608 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21014 4800 5 %RANDOM
Rwork0.17933 ---
obs0.18089 91006 97.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.645 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å20.07 Å20.05 Å2
2--0.42 Å2-1.03 Å2
3---0.97 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6552 0 114 458 7124
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0196840
X-RAY DIFFRACTIONr_bond_other_d0.0010.026692
X-RAY DIFFRACTIONr_angle_refined_deg1.2131.9549212
X-RAY DIFFRACTIONr_angle_other_deg0.8882.98715474
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4185836
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.08326.376298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.544151283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.288156
X-RAY DIFFRACTIONr_chiral_restr0.0750.21048
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027599
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021479
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_it1.2712.363314
X-RAY DIFFRACTIONr_mcbond_other1.2712.3593313
X-RAY DIFFRACTIONr_mcangle_it2.1093.5294151
X-RAY DIFFRACTIONr_mcangle_other2.1093.5314152
X-RAY DIFFRACTIONr_scbond_it1.6672.6843526
X-RAY DIFFRACTIONr_scbond_other1.6662.6843526
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7783.9065059
X-RAY DIFFRACTIONr_long_range_B_refined4.65719.4897829
X-RAY DIFFRACTIONr_long_range_B_other4.51819.2557680
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
Rfree0.304 357 -
Rwork0.283 6644 -
obs--96.49 %

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