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- PDB-9jzd: PfDXR - Mn2+ - NADPH - MAMK433 quaternary complex -

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Basic information

Entry
Database: PDB / ID: 9jzd
TitlePfDXR - Mn2+ - NADPH - MAMK433 quaternary 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
: / : / Chem-NDP / 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: 1.65 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)114,16311
Polymers111,6592
Non-polymers2,5049
Water9,512528
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-56 kcal/mol
Surface area32800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.596, 76.699, 110.165
Angle α, β, γ (deg.)90.00, 92.77, 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, 537 molecules

#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical ChemComp-A1L44 / [(1~{S})-4-[3-(4-methylphenyl)propyl-oxidanyl-amino]-4-oxidanylidene-1-phenyl-butyl]phosphonic acid


Mass: 391.398 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H26NO5P / Feature type: SUBJECT OF INVESTIGATION
#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.: 528 / 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: 2.06 Å3/Da / Density % sol: 40.24 %
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: Photon Factory / Beamline: BL-1A / Wavelength: 1.012 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.012 Å / Relative weight: 1
ReflectionResolution: 1.65→62.92 Å / Num. obs: 101361 / % possible obs: 98.2 % / Redundancy: 4 % / CC1/2: 0.977 / Net I/σ(I): 5.3
Reflection shellResolution: 1.65→1.68 Å / Num. unique obs: 4800 / CC1/2: 0.534

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
xia2data reduction
Cootmodel building
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.65→62.92 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.101 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20665 5080 5 %RANDOM
Rwork0.17867 ---
obs0.18007 96139 98.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.941 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å2-0 Å2-0.55 Å2
2--0.29 Å2-0 Å2
3---0.43 Å2
Refinement stepCycle: 1 / Resolution: 1.65→62.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6518 0 155 528 7201
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0126798
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166547
X-RAY DIFFRACTIONr_angle_refined_deg1.7451.829196
X-RAY DIFFRACTIONr_angle_other_deg0.5851.77615148
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3635812
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.298516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.566101272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0860.21050
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027596
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021443
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_it1.8731.7583260
X-RAY DIFFRACTIONr_mcbond_other1.8731.7583260
X-RAY DIFFRACTIONr_mcangle_it2.883.1444068
X-RAY DIFFRACTIONr_mcangle_other2.883.1464069
X-RAY DIFFRACTIONr_scbond_it3.0572.2263538
X-RAY DIFFRACTIONr_scbond_other3.0572.2263539
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8683.9035129
X-RAY DIFFRACTIONr_long_range_B_refined6.64719.618076
X-RAY DIFFRACTIONr_long_range_B_other6.56218.727953
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.692 Å
RfactorNum. reflection% reflection
Rfree0.343 341 -
Rwork0.317 6831 -
obs--94.64 %
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)
10.1340.07370.05130.09070.15680.36140.01850.0144-0.02990.01810.0028-0.01110.0363-0.0155-0.02130.0099-0.0004-0.02270.0243-0.01010.07510.6117-16.106712.9807
20.1893-0.01760.14030.10360.06870.2221-0.0346-0.01950.003-0.00370.02820.004-0.0240.01540.00640.0115-0.0018-0.01290.0391-0.00460.053216.129114.874139.5885
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A76 - 486
2X-RAY DIFFRACTION2B76 - 486

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