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- PDB-6aj6: Crystal structure of Trypanosoma brucei glycosomal isocitrate deh... -

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Basic information

Entry
Database: PDB / ID: 6aj6
TitleCrystal structure of Trypanosoma brucei glycosomal isocitrate dehydrogenase in complex with NADP+
ComponentsIsocitrate dehydrogenase [NADP]
KeywordsOXIDOREDUCTASE / Trypanosoma brucei / glycosome / metabolism / isocitrate dehydrogenase
Function / homology
Function and homology information


isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / NADP+ metabolic process / glycosome / tricarboxylic acid cycle / NAD binding / magnesium ion binding / mitochondrion
Similarity search - Function
Isocitrate dehydrogenase NADP-dependent / Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isocitrate and isopropylmalate dehydrogenases signature. / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Isocitrate dehydrogenase [NADP]
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsWang, X. / Inaoka, D.K. / Shiba, T. / Balogun, E.O. / Ziebart, N. / Allman, S. / Watanabe, Y. / Nozaki, T. / Boshart, M. / Bringaud, F. ...Wang, X. / Inaoka, D.K. / Shiba, T. / Balogun, E.O. / Ziebart, N. / Allman, S. / Watanabe, Y. / Nozaki, T. / Boshart, M. / Bringaud, F. / Harada, S. / Kita, K.
CitationJournal: To Be Published
Title: Biochemical characterization of a novel Trypanosoma brucei glycosomal isocitrate dehydrogenase with dual coenzyme specificity (NADP+/NAD+)
Authors: Wang, X. / Inaoka, D.K. / Shiba, T. / Balogun, E.O. / Ziebart, N. / Allman, S. / Watanabe, Y. / Nozaki, T. / Boshart, M. / Bringaud, F. / Harada, S. / Kita, K.
History
DepositionAug 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isocitrate dehydrogenase [NADP]
C: Isocitrate dehydrogenase [NADP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0704
Polymers93,5832
Non-polymers1,4872
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8100 Å2
ΔGint-55 kcal/mol
Surface area36010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.442, 109.754, 64.961
Angle α, β, γ (deg.)90.00, 89.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Isocitrate dehydrogenase [NADP]


Mass: 46791.590 Da / Num. of mol.: 2 / Mutation: M1S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: ILtat 1.4 / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli)
References: UniProt: Q387G0, isocitrate dehydrogenase (NADP+)
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
Sequence detailsThe sequence was derived from Trypanosome brucei brucei ILtat 1.4. However, the sequence reference ...The sequence was derived from Trypanosome brucei brucei ILtat 1.4. However, the sequence reference available at uniprot at the time of data processing was derived from a different strain TRYPANOSOMA BRUCEI BRUCEI (STRAIN 927/4 GUTAT10.1) (taxonomy ID 185431).

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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: 2.38 Å3/Da / Density % sol: 48.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: 20% PEG 3350, 200mM potassium nitrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.609
11h,-k,-l20.391
ReflectionResolution: 3.2→50 Å / Num. obs: 14385 / % possible obs: 98.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 6.6
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.799 / Mean I/σ(I) obs: 1.45 / Num. unique obs: 753 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T0L

1t0l


Resolution: 3.2→45.02 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.817 / SU B: 28.305 / SU ML: 0.44 / Cross valid method: THROUGHOUT / ESU R Free: 0.171 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30858 558 4.6 %RANDOM
Rwork0.21219 ---
obs0.21649 11582 83.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 79.105 Å2
Baniso -1Baniso -2Baniso -3
1-20.92 Å20 Å226.33 Å2
2---17.14 Å2-0 Å2
3----3.79 Å2
Refinement stepCycle: 1 / Resolution: 3.2→45.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6564 0 96 0 6660
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196804
X-RAY DIFFRACTIONr_bond_other_d0.0030.026466
X-RAY DIFFRACTIONr_angle_refined_deg1.8751.9699208
X-RAY DIFFRACTIONr_angle_other_deg1.138314888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.415824
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.71623.6300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.999151204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8271546
X-RAY DIFFRACTIONr_chiral_restr0.0970.21018
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027548
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021564
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_it4.5937.1363302
X-RAY DIFFRACTIONr_mcbond_other4.5927.1343301
X-RAY DIFFRACTIONr_mcangle_it7.73510.6784124
X-RAY DIFFRACTIONr_mcangle_other7.73410.6814125
X-RAY DIFFRACTIONr_scbond_it3.6827.4163502
X-RAY DIFFRACTIONr_scbond_other3.6827.4163503
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.31710.9835085
X-RAY DIFFRACTIONr_long_range_B_refined11.72357.148232
X-RAY DIFFRACTIONr_long_range_B_other11.72257.1448233
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.281 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 9 -
Rwork0.262 253 -
obs--25 %
Refinement TLS params.Method: refined / Origin x: 26.8163 Å / Origin y: -1.1513 Å / Origin z: 17.713 Å
111213212223313233
T0.1671 Å2-0.0096 Å2-0.0685 Å2-0.1136 Å2-0.0172 Å2--0.0509 Å2
L0.3735 °20.6421 °20.0528 °2-1.2718 °20.0822 °2--0.0133 °2
S-0.0688 Å °0.1068 Å °-0.0792 Å °0.1104 Å °0.1133 Å °-0.2108 Å °-0.0198 Å °-0.0038 Å °-0.0445 Å °

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