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- PDB-9kp9: PfDXR - Mn2+ - NADPH - TAKK443 quaternary complex -

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Basic information

Entry
Database: PDB / ID: 9kp9
TitlePfDXR - Mn2+ - NADPH - TAKK443 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: 2.13 Å
AuthorsTakada, S. / Sakamoto, Y. / Tanaka, N.
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
DepositionNov 22, 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)57,0214
Polymers55,8301
Non-polymers1,1923
Water3,567198
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)114,0438
Polymers111,6592
Non-polymers2,3846
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area6280 Å2
ΔGint-34 kcal/mol
Surface area31390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.498, 92.498, 105.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#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.: 1
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
#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-A1L6A / [(~{S})-(3-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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
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: 2.33 Å3/Da / Density % sol: 47.1 %
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: 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: 2.13→80.11 Å / Num. obs: 29428 / % possible obs: 99.5 % / Redundancy: 6.7 % / Biso Wilson estimate: 26.76 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.06 / Rrim(I) all: 0.159 / Net I/σ(I): 7.8
Reflection shellResolution: 2.13→2.17 Å / Rmerge(I) obs: 0.982 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1440 / CC1/2: 0.527 / Rpim(I) all: 0.429 / Rrim(I) all: 1.077

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
xia2data reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.13→80.11 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.944 / SU B: 9.658 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20557 1495 5.1 %RANDOM
Rwork0.16641 ---
obs0.16841 27903 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.694 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å2-0.18 Å20 Å2
2---0.35 Å2-0 Å2
3---1.14 Å2
Refinement stepCycle: 1 / Resolution: 2.13→80.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3286 0 74 198 3558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0123426
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163297
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.824636
X-RAY DIFFRACTIONr_angle_other_deg0.5411.7777633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3745410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.37158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.04410641
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0770.2528
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023826
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_it1.8152.2121643
X-RAY DIFFRACTIONr_mcbond_other1.8112.2111643
X-RAY DIFFRACTIONr_mcangle_it2.8493.9642052
X-RAY DIFFRACTIONr_mcangle_other2.8483.9662053
X-RAY DIFFRACTIONr_scbond_it2.6642.5991783
X-RAY DIFFRACTIONr_scbond_other2.6632.6011784
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2084.6342585
X-RAY DIFFRACTIONr_long_range_B_refined6.27622.423978
X-RAY DIFFRACTIONr_long_range_B_other6.221.73945
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.13→2.185 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 88 -
Rwork0.26 2057 -
obs--99.35 %
Refinement TLS params.Method: refined / Origin x: 32.0609 Å / Origin y: 7.3046 Å / Origin z: 14.0985 Å
111213212223313233
T0.0834 Å20.0278 Å2-0.0384 Å2-0.0484 Å2-0.0244 Å2--0.0412 Å2
L0.8728 °2-0.0379 °20.135 °2-1.5407 °2-0.443 °2--1.3351 °2
S0.0755 Å °0.1679 Å °-0.1186 Å °-0.3394 Å °-0.049 Å °0.1589 Å °0.1035 Å °-0.0753 Å °-0.0265 Å °

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