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- PDB-4gae: Crystal structure of plasmodium dxr in complex with a pyridine-co... -

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Basic information

Entry
Database: PDB / ID: 4gae
TitleCrystal structure of plasmodium dxr in complex with a pyridine-containing inhibitor
Components1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplast
KeywordsISOMERASE/ISOMERASE INHIBITOR / NADPH BINDING / ISOMERASE-ISOMERASE INHIBITOR complex
Function / homology
Function and homology information


apicoplast / 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 / 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 / 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
ACETATE ION / Chem-FOB / Chem-FOQ / : / Chem-NDP / 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDiao, J. / Xue, J. / Cai, G. / Deng, L. / Song, Y.
CitationJournal: ACS Med Chem Lett / Year: 2013
Title: Antimalarial and Structural Studies of Pyridine-containing Inhibitors of 1-Deoxyxylulose-5-phosphate Reductoisomerase.
Authors: Xue, J. / Diao, J. / Cai, G. / Deng, L. / Zheng, B. / Yao, Y. / Song, Y.
History
DepositionJul 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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)100,22518
Polymers97,0782
Non-polymers3,14716
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7570 Å2
ΔGint-52 kcal/mol
Surface area32040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.360, 77.280, 109.410
Angle α, β, γ (deg.)90.00, 91.50, 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, apicoplast / 1-deoxyxylulose-5-phosphate reductoisomerase / DOXP reductoisomerase / DXP reductoisomerase


Mass: 48538.848 Da / Num. of mol.: 2 / Mutation: L247I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: DXR / Plasmid: pQE30 / Production host: Escherichia coli (E. coli)
References: UniProt: O96693, 1-deoxy-D-xylulose-5-phosphate reductoisomerase

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Non-polymers , 8 types, 154 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
#3: Chemical ChemComp-FOB / [(1R)-3-[acetyl(hydroxy)amino]-1-(pyridin-4-yl)propyl]phosphonic acid


Mass: 274.210 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N2O5P
#4: Chemical ChemComp-FOQ / [(1S)-3-[acetyl(hydroxy)amino]-1-(pyridin-4-yl)propyl]phosphonic acid


Mass: 274.210 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N2O5P
#5: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O

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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: 2.24 Å3/Da / Density % sol: 44.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: The protein solution containing 10 mg/mL PfDXR, 2 mM inhibitor, 3 mM NADPH, 2 mM MnCl2, 2 mM DTT, 50 mM Tris, pH 7.8 was mixed with an equal volume of the reservoir solution of 0.1 M Tris, ...Details: The protein solution containing 10 mg/mL PfDXR, 2 mM inhibitor, 3 mM NADPH, 2 mM MnCl2, 2 mM DTT, 50 mM Tris, pH 7.8 was mixed with an equal volume of the reservoir solution of 0.1 M Tris, pH 8.0, 20% PEG 3350, 0.3 M CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Aug 26, 2011 / Details: Mirrors
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.3→51.34 Å / Num. obs: 34047 / % possible obs: 89.2 % / Redundancy: 3.9 % / Biso Wilson estimate: 32.94 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 15.6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.125 / Mean I/σ(I) obs: 6.9 / Num. unique all: 3590 / % possible all: 64.8

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
CNS1.3refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AU9

3au9


Resolution: 2.3→44.64 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1797958.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1698 5 %RANDOM
Rwork0.23 ---
obs0.23 34035 89 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 2.98149 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso mean: 37.3 Å2
Baniso -1Baniso -2Baniso -3
1--3.79 Å20 Å2-5.39 Å2
2---0.92 Å20 Å2
3---4.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.3→44.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6600 0 193 138 6931
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it2.242
X-RAY DIFFRACTIONc_scbond_it2.122
X-RAY DIFFRACTIONc_scangle_it3.052.5
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.32 130 5.6 %
Rwork0.247 2191 -
obs-2321 61.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6NDP_par.txtNDP_top.txt
X-RAY DIFFRACTION7FAEQ_par.txtFAEQ_top.txt

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