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- PDB-6aj8: Crystal structure of Trypanosoma brucei glycosomal isocitrate deh... -

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Basic information

Entry
Database: PDB / ID: 6aj8
TitleCrystal structure of Trypanosoma brucei glycosomal isocitrate dehydrogenase in complex 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
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
2-OXOGLUTARIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Isocitrate dehydrogenase [NADP]
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 ...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
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_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_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)95,2967
Polymers93,5832
Non-polymers1,7135
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8940 Å2
ΔGint-82 kcal/mol
Surface area34630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.474, 112.021, 132.136
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 25% PEG 1500, 100mM PCB buffer

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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: Apr 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 34871 / % possible obs: 98.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 9.6
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3339 / % possible all: 98.6

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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: 6AJ6

6aj6


Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.902 / SU B: 22.856 / SU ML: 0.267 / Cross valid method: THROUGHOUT / ESU R: 0.798 / ESU R Free: 0.32 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27058 1596 4.9 %RANDOM
Rwork0.21671 ---
obs0.21939 30973 93.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 51.845 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å2-0 Å20 Å2
2--0.83 Å2-0 Å2
3---0.17 Å2
Refinement stepCycle: 1 / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6564 0 108 233 6905
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196840
X-RAY DIFFRACTIONr_bond_other_d0.0020.026478
X-RAY DIFFRACTIONr_angle_refined_deg1.671.9699261
X-RAY DIFFRACTIONr_angle_other_deg1.066314916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5645830
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.16423.553304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.576151205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1061548
X-RAY DIFFRACTIONr_chiral_restr0.0970.21019
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027621
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021577
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_it0.9192.4633317
X-RAY DIFFRACTIONr_mcbond_other0.9192.4613316
X-RAY DIFFRACTIONr_mcangle_it1.6663.6894148
X-RAY DIFFRACTIONr_mcangle_other1.6653.6924149
X-RAY DIFFRACTIONr_scbond_it0.7232.5483523
X-RAY DIFFRACTIONr_scbond_other0.7132.5413519
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2973.7715110
X-RAY DIFFRACTIONr_long_range_B_refined4.24219.47868
X-RAY DIFFRACTIONr_long_range_B_other4.17219.3417840
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 78 -
Rwork0.263 1653 -
obs--69.21 %
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)
11.1256-0.1714-0.00572.32111.11491.0755-0.26920.2007-0.37910.31870.20430.40460.0494-0.00310.06490.1525-0.03080.11630.10920.01520.22554.238996.0287-48.5975
20.25780.303-0.06973.37470.6771.0725-0.20970.01970.0165-0.30870.5591-0.5737-0.17320.0139-0.34940.22250.00290.04650.1294-0.08660.165523.9333127.326-47.3006
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 413
2X-RAY DIFFRACTION1A501
3X-RAY DIFFRACTION2B1 - 413
4X-RAY DIFFRACTION2B501

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