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- PDB-9job: PfDXR - Mn2+ - NADPH - MAMK89 quaternary complex -

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Basic information

Entry
Database: PDB / ID: 9job
TitlePfDXR - Mn2+ - NADPH - MAMK89 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 / FOURIER SYNTHESIS / Resolution: 1.39 Å
AuthorsTakada, S. / Sakamoto, Y. / Tanaka, N.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)120223508 Japan
CitationJournal: ACS Infect Dis / Year: 2024
Title: Reverse N-Substituted Hydroxamic Acid Derivatives of Fosmidomycin Target a Previously Unknown Subpocket of 1-Deoxy-d-xylulose 5-Phosphate Reductoisomerase (DXR)
Authors: Abdullaziz, M.A. / Takada, S. / Illarionov, B. / Pessanha de Carvalho, L. / Sakamoto, Y. / Hoefmann, S. / Knak, T. / Kiffe-Delf, A.L. / Mazzone, F. / Pfeffer, K. / Kalscheuer, R. / Bacher, A. ...Authors: Abdullaziz, M.A. / Takada, S. / Illarionov, B. / Pessanha de Carvalho, L. / Sakamoto, Y. / Hoefmann, S. / Knak, T. / Kiffe-Delf, A.L. / Mazzone, F. / Pfeffer, K. / Kalscheuer, R. / Bacher, A. / Held, J. / Fischer, M. / Tanaka, N. / Kurz, T.
History
DepositionSep 24, 2024Deposition site: PDBJ / Processing site: PDBJ
SupersessionJan 1, 2025ID: 8JNW
Revision 1.0Jan 1, 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)114,13511
Polymers111,6592
Non-polymers2,4769
Water11,872659
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6660 Å2
ΔGint-57 kcal/mol
Surface area31460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.518, 78.201, 111.144
Angle α, β, γ (deg.)90.00, 92.64, 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


Mass: 55829.609 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 668 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-UW0 / [(1~{S})-4-oxidanylidene-4-[oxidanyl(3-phenylpropyl)amino]-1-phenyl-butyl]phosphonic acid


Mass: 377.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H24NO5P / 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.: 659 / 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 Å3/Da / Density % sol: 38.59 %
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-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.39→63.93 Å / Num. obs: 164006 / % possible obs: 92.7 % / Redundancy: 6.3 % / Biso Wilson estimate: 17.14 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.028 / Rrim(I) all: 0.072 / Net I/σ(I): 10.9
Reflection shellResolution: 1.39→1.41 Å / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4569 / CC1/2: 0.582 / Rpim(I) all: 0.537 / Rrim(I) all: 1.116

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.39→63.93 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.99 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18919 8391 5.1 %RANDOM
Rwork0.16512 ---
obs0.16632 155538 92.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.431 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å2-0.42 Å2
2--0.3 Å20 Å2
3----0.48 Å2
Refinement stepCycle: 1 / Resolution: 1.39→63.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6570 0 153 659 7382
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0126854
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166586
X-RAY DIFFRACTIONr_angle_refined_deg2.0421.8219274
X-RAY DIFFRACTIONr_angle_other_deg0.6491.77515248
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0295820
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.281516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.643101282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1020.21056
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027668
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021458
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_it2.1431.8823286
X-RAY DIFFRACTIONr_mcbond_other2.1421.8823286
X-RAY DIFFRACTIONr_mcangle_it3.0633.3774104
X-RAY DIFFRACTIONr_mcangle_other3.0633.3794105
X-RAY DIFFRACTIONr_scbond_it3.2892.2943568
X-RAY DIFFRACTIONr_scbond_other3.2892.2943569
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9824.035171
X-RAY DIFFRACTIONr_long_range_B_refined6.5520.598065
X-RAY DIFFRACTIONr_long_range_B_other6.47119.387904
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.39→1.425 Å
RfactorNum. reflection% reflection
Rfree0.32 355 -
Rwork0.297 6745 -
obs--54.64 %
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)
10.12290.11610.14850.2070.32370.52570.04310.04-0.03590.0519-0.0022-0.03080.0727-0.0241-0.04090.01690.0085-0.0110.0405-0.02720.02910.7451-16.252213.0108
20.16890.00810.18960.1560.13840.3202-0.0373-0.0158-0.0144-0.01780.04110.0131-0.05560.0157-0.00380.011-0.00590.00330.0451-0.00440.005116.315914.89439.8862
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A76 - 486
2X-RAY DIFFRACTION2B76 - 486

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