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- PDB-8zxx: PfDXR - Mn2+ - NADPH - TAKK442 quaternary complex -

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Basic information

Entry
Database: PDB / ID: 8zxx
TitlePfDXR - Mn2+ - NADPH - TAKK442 quaternary complex
Components1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic
KeywordsISOMERASE / 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 HB3 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 Å
AuthorsTanaka, N. / Takada, S. / Sakamoto, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Acs Med.Chem.Lett. / Year: 2025
Title: Expanding the Chemical Space of Reverse Fosmidomycin Analogs.
Authors: Knak, T. / Takada, S. / Illarionov, B. / Krisilia, V. / Pessanha de Carvalho, L. / Lungerich, B. / Sakamoto, Y. / Hofmann, S. / Bacher, A. / Kalscheuer, R. / Held, J. / Fischer, M. / Tanaka, N. / Kurz, T.
History
DepositionJun 15, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,4175
Polymers47,1331
Non-polymers1,2844
Water6,485360
1
A: 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)96,83410
Polymers94,2672
Non-polymers2,5688
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Buried area6870 Å2
ΔGint-38 kcal/mol
Surface area31610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.616, 92.616, 105.043
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 47133.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum HB3 (eukaryote) / 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, 364 molecules

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


Mass: 745.421 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-A1L2H / [(~{S})-(4-hexoxyphenyl)-[2-[methyl(oxidanyl)amino]-2-oxidanylidene-ethyl]sulfanyl-methyl]phosphonic acid


Mass: 391.420 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H26NO6PS / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.76 Å3/Da / Density % sol: 55.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.08 M MES-NaOH pH 6.0, 16%(w/v) PEG6000, and 0.16 M NaCl

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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: Jul 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.23→42.37 Å / Num. obs: 150636 / % possible obs: 99.8 % / Redundancy: 4 % / Biso Wilson estimate: 14.49 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.066 / Rrim(I) all: 0.136 / Net I/σ(I): 6.4
Reflection shellResolution: 1.23→1.25 Å / Redundancy: 4 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 7387 / CC1/2: 0.538 / Rpim(I) all: 0.543 / Rrim(I) all: 1.097 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.23→42.37 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.184 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17804 7600 5.1 %RANDOM
Rwork0.16691 ---
obs0.16747 142829 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.026 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0.05 Å20 Å2
2---0.1 Å2-0 Å2
3---0.32 Å2
Refinement stepCycle: 1 / Resolution: 1.23→42.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3286 0 80 360 3726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0123431
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163303
X-RAY DIFFRACTIONr_angle_refined_deg1.9241.8194641
X-RAY DIFFRACTIONr_angle_other_deg0.6231.7767647
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9325410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.94758
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.58210641
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0990.2529
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023826
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02721
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_it1.581.5991643
X-RAY DIFFRACTIONr_mcbond_other1.581.5981643
X-RAY DIFFRACTIONr_mcangle_it2.3772.8712052
X-RAY DIFFRACTIONr_mcangle_other2.382.8742053
X-RAY DIFFRACTIONr_scbond_it2.9071.9811788
X-RAY DIFFRACTIONr_scbond_other2.9061.9811789
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4623.4712590
X-RAY DIFFRACTIONr_long_range_B_refined5.59318.283996
X-RAY DIFFRACTIONr_long_range_B_other5.4715.873900
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.23→1.262 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 570 -
Rwork0.291 10435 -
obs--99.59 %
Refinement TLS params.Method: refined / Origin x: 32.1688 Å / Origin y: 7.3344 Å / Origin z: 14.0211 Å
111213212223313233
T0.035 Å20.023 Å2-0.0071 Å2-0.0241 Å2-0.0094 Å2--0.0079 Å2
L0.1431 °2-0.0997 °2-0.0164 °2-0.2662 °2-0.0523 °2--0.112 °2
S0.0439 Å °0.017 Å °-0.0181 Å °-0.0642 Å °-0.0615 Å °0.0261 Å °-0.0004 Å °-0.0083 Å °0.0176 Å °

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