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- PDB-4y67: Structure of Plasmodium falciparum DXR in complex with a beta-sub... -

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Basic information

Entry
Database: PDB / ID: 4y67
TitleStructure of Plasmodium falciparum DXR in complex with a beta-substituted fosmidomycin analogue, RC176, and manganese
Components1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplast
KeywordsOXIDOREDUCTASE / enzyme-inhibitor complex / MEP pathway / isoprenoid biosynthesis
Function / homology
Function and homology information


apicoplast / 1-deoxy-D-xylulose-5-phosphate reductoisomerase / 1-deoxy-D-xylulose-5-phosphate reductoisomerase activity / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / NADPH binding / metal 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 / RNA polymerase sigma factor, region 2, helix turn helix motif / Rna Polymerase Sigma Factor; Chain: A ...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 / RNA polymerase sigma factor, region 2, helix turn helix motif / Rna Polymerase Sigma Factor; Chain: A / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Chem-RC5 / 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSooriyaarachchi, S. / Bergfors, T. / Jones, T.A. / Mowbray, S.L.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Vetenskapsradet Sweden
CitationJournal: J.Med.Chem. / Year: 2015
Title: Synthesis and Bioactivity of beta-Substituted Fosmidomycin Analogues Targeting 1-Deoxy-d-xylulose-5-phosphate Reductoisomerase.
Authors: Chofor, R. / Sooriyaarachchi, S. / Risseeuw, M.D. / Bergfors, T. / Pouyez, J. / Johny, C. / Haymond, A. / Everaert, A. / Dowd, C.S. / Maes, L. / Coenye, T. / Alex, A. / Couch, R.D. / Jones, ...Authors: Chofor, R. / Sooriyaarachchi, S. / Risseeuw, M.D. / Bergfors, T. / Pouyez, J. / Johny, C. / Haymond, A. / Everaert, A. / Dowd, C.S. / Maes, L. / Coenye, T. / Alex, A. / Couch, R.D. / Jones, T.A. / Wouters, J. / Mowbray, S.L. / Van Calenbergh, S.
History
DepositionFeb 12, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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, apicoplast
B: 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplast
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,0696
Polymers96,3292
Non-polymers7404
Water12,863714
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-18 kcal/mol
Surface area32600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.570, 56.465, 86.024
Angle α, β, γ (deg.)104.11, 103.25, 100.16
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 1 / Auth seq-ID: 77 - 486 / Label seq-ID: 11 - 420

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplast / DXP reductoisomerase


Mass: 48164.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Mature protein lacks signal and apicoplast targeting sequences
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: DXR, PF14_0641 / Plasmid: pEXP-5-CT/TOPO / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43
References: UniProt: Q8IKG4, 1-deoxy-D-xylulose-5-phosphate reductoisomerase
#2: Chemical ChemComp-RC5 / [(2R)-2-{2-[hydroxy(methyl)amino]-2-oxoethyl}-5-phenylpentyl]phosphonic acid


Mass: 315.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H22NO5P
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 714 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.02M each of sodium L-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine, 0.1M mes/imidazole pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97856 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2014 / Details: mirrors
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.6→79.97 Å / Num. all: 110454 / Num. obs: 110454 / % possible obs: 94.2 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.2
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 2.1 / % possible all: 90.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AU8

3au8


Resolution: 1.6→48.65 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.284 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2062 5530 5 %RANDOM
Rwork0.1766 ---
obs0.17807 104856 94.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.628 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å2-0.71 Å20.23 Å2
2--0.07 Å2-1.59 Å2
3---1.68 Å2
Refinement stepCycle: LAST / Resolution: 1.6→48.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6552 0 44 714 7310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196831
X-RAY DIFFRACTIONr_bond_other_d0.0020.026629
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.9569237
X-RAY DIFFRACTIONr_angle_other_deg0.7662.99415347
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5255848
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.49926.424302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.587151289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.58156
X-RAY DIFFRACTIONr_chiral_restr0.0790.21053
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027680
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021494
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_it1.4822.023335
X-RAY DIFFRACTIONr_mcbond_other1.4812.0193334
X-RAY DIFFRACTIONr_mcangle_it2.3213.024184
X-RAY DIFFRACTIONr_mcangle_other2.3213.0224185
X-RAY DIFFRACTIONr_scbond_it2.1282.3513496
X-RAY DIFFRACTIONr_scbond_other2.1272.3513497
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.473.4085048
X-RAY DIFFRACTIONr_long_range_B_refined5.77317.7878595
X-RAY DIFFRACTIONr_long_range_B_other5.58617.3548284
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCSNumber: 3948 / Type: tight thermal / Rms dev position: 2.29 Å / Weight position: 0.5
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 388 -
Rwork0.265 7345 -
obs--89.4 %

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