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- PDB-7e3n: Crystal structure of Isocitrate dehydrogenase D252N mutant from T... -

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Basic information

Entry
Database: PDB / ID: 7e3n
TitleCrystal structure of Isocitrate dehydrogenase D252N mutant from Trypanosoma brucei in complexed with NADP+, alpha-ketoglutarate, and ca2+
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 / cytosol
Similarity search - Function
Isocitrate dehydrogenase NADP-dependent / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isocitrate and isopropylmalate dehydrogenases signature. / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase
Similarity search - Domain/homology
ISOCITRIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Isocitrate dehydrogenase [NADP]
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsArai, N. / Shiba, T. / Inaoka, D.K. / Kita, K. / Wang, X. / Otani, M. / Matsushiro, S. / Kojima, C.
CitationJournal: To Be Published
Title: Crystal structure of Isocitrate dehydrogenase from Trypanosoma brucei.
Authors: Arai, N. / Shiba, T. / Inaoka, D.K. / Kita, K. / Wang, X. / Otani, M. / Matsushiro, S. / Kojima, C.
History
DepositionFeb 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isocitrate dehydrogenase [NADP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7664
Polymers46,7911
Non-polymers9763
Water1,56787
1
A: Isocitrate dehydrogenase [NADP]
hetero molecules

A: Isocitrate dehydrogenase [NADP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5328
Polymers93,5812
Non-polymers1,9516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area10490 Å2
ΔGint-78 kcal/mol
Surface area31230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.267, 89.767, 62.031
Angle α, β, γ (deg.)90.00, 121.04, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-673-

HOH

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Components

#1: Protein Isocitrate dehydrogenase [NADP]


Mass: 46790.605 Da / Num. of mol.: 1 / Mutation: M1S, D252N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (strain 927/4 GUTat10.1) (eukaryote)
Strain: 927/4 GUTat10.1 / Gene: Tb11.03.0230 / 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.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ICT / ISOCITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.68 Å3/Da / Density % sol: 54.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 14% PEG6000,100MM HEPES BUFFER / PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 25, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→18.94 Å / Num. obs: 39065 / % possible obs: 99.1 % / Redundancy: 5.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.07 / Net I/σ(I): 14.79
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 3.61 / Num. unique obs: 6256 / CC1/2: 0.932 / Rrim(I) all: 0.551 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AJA

6aja


Resolution: 1.9→18.94 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.403 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23721 1962 5 %RANDOM
Rwork0.20528 ---
obs0.20687 37060 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.912 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.9→18.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3191 0 62 87 3340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193323
X-RAY DIFFRACTIONr_bond_other_d0.0010.023136
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.974500
X-RAY DIFFRACTIONr_angle_other_deg0.83237215
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.925400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.48423.423149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.86515576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8521524
X-RAY DIFFRACTIONr_chiral_restr0.0990.2496
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023693
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02772
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_it1.693.2671603
X-RAY DIFFRACTIONr_mcbond_other1.6873.2661602
X-RAY DIFFRACTIONr_mcangle_it2.5094.8932002
X-RAY DIFFRACTIONr_mcangle_other2.5094.8952003
X-RAY DIFFRACTIONr_scbond_it1.9143.4731720
X-RAY DIFFRACTIONr_scbond_other1.9113.4741718
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0535.1132498
X-RAY DIFFRACTIONr_long_range_B_refined4.10425.7173770
X-RAY DIFFRACTIONr_long_range_B_other4.10225.7123741
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.944 Å
RfactorNum. reflection% reflection
Rfree0.312 173 -
Rwork0.286 2638 -
obs--97.81 %

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