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- PDB-9jz9: PfDXR - Mn2+ - MAMK218 ternary complex -

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Basic information

Entry
Database: PDB / ID: 9jz9
TitlePfDXR - Mn2+ - MAMK218 ternary complex
Components1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic
KeywordsISOMERASE / Inhibitor / Malaria
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 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / : / 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: 1.33 Å
AuthorsTakada, S. / Sakamoto, Y. / Tanaka, N.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Molecules / Year: 2024
Title: The Diverse Binding Modes Explain the Nanomolar Levels of Inhibitory Activities Against 1-Deoxy-d-Xylulose 5-Phosphate Reductoisomerase from Plasmodium falciparum Exhibited by Reverse ...Title: The Diverse Binding Modes Explain the Nanomolar Levels of Inhibitory Activities Against 1-Deoxy-d-Xylulose 5-Phosphate Reductoisomerase from Plasmodium falciparum Exhibited by Reverse Hydroxamate Analogs of Fosmidomycin with Varying N -Substituents.
Authors: Takada, S. / Abdullaziz, M.A. / Hofmann, S. / Knak, T. / Ozawa, S.I. / Sakamoto, Y. / Kurz, T. / Tanaka, N.
History
DepositionOct 14, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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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)112,85611
Polymers111,6592
Non-polymers1,1979
Water12,106672
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-44 kcal/mol
Surface area33170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.934, 77.572, 111.659
Angle α, β, γ (deg.)90.00, 93.20, 90.00
Int Tables number4
Space group name H-MP1211

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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 / 1-deoxyxylulose-5-phosphate reductoisomerase / DOXP reductoisomerase / DXP reductoisomerase


Mass: 55829.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: DXR / Production host: Escherichia coli (E. coli)
References: UniProt: O96693, 1-deoxy-D-xylulose-5-phosphate reductoisomerase

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Non-polymers , 5 types, 681 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1L41 / [(1~{S})-4-oxidanylidene-4-[oxidanyl(4-phenylbutyl)amino]-1-phenyl-butyl]phosphonic acid


Mass: 391.398 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H26NO5P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 672 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.01 Å3/Da / Density % sol: 38.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl pH 8.0, 20%(w/v) PEG6000, and 0.2 M CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.33→46.04 Å / Num. obs: 201013 / % possible obs: 98.8 % / Redundancy: 3 % / CC1/2: 0.995 / Net I/σ(I): 8
Reflection shellResolution: 1.33→1.35 Å / Num. unique obs: 9331 / CC1/2: 0.556

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
xia2data reduction
Cootmodel building
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.33→46.04 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.853 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18993 10106 5 %RANDOM
Rwork0.16944 ---
obs0.17047 190744 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.789 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å2-0 Å2-0.19 Å2
2--0.28 Å20 Å2
3---0.17 Å2
Refinement stepCycle: 1 / Resolution: 1.33→46.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6518 0 71 672 7261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0126776
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166560
X-RAY DIFFRACTIONr_angle_refined_deg1.931.8199146
X-RAY DIFFRACTIONr_angle_other_deg0.661.78115174
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0595818
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2.42556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.621101276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1020.21036
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027646
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021472
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_it1.751.4573278
X-RAY DIFFRACTIONr_mcbond_other1.7491.4573278
X-RAY DIFFRACTIONr_mcangle_it2.612.6144094
X-RAY DIFFRACTIONr_mcangle_other2.6112.6154095
X-RAY DIFFRACTIONr_scbond_it3.231.9423498
X-RAY DIFFRACTIONr_scbond_other3.2291.9423499
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0713.3575053
X-RAY DIFFRACTIONr_long_range_B_refined6.74116.677842
X-RAY DIFFRACTIONr_long_range_B_other6.6415.687693
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.33→1.362 Å
RfactorNum. reflection% reflection
Rfree0.315 722 -
Rwork0.301 13359 -
obs--93.91 %
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)
10.13340.040.01810.12120.23030.4687-0.0060.0242-0.0380.0298-0.0116-0.00140.0519-0.03420.01760.0552-0.0026-0.00640.0545-0.020.01670.5287-16.352713.3103
20.1673-0.01650.09130.11760.09830.1584-0.0284-0.02280.0082-0.01310.02750.0025-0.01380.01650.0010.0383-0.0046-0.01180.0806-0.00860.00516.078215.085240.0554
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A76 - 486
2X-RAY DIFFRACTION2B76 - 486

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