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- PDB-6ajc: Crystal structure of Trypanosoma cruzi cytosolic isocitrate dehyd... -

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Basic information

Entry
Database: PDB / ID: 6ajc
TitleCrystal structure of Trypanosoma cruzi cytosolic isocitrate dehydrogenase in complex with NADP+, isocitrate and ca2+
ComponentsIsocitrate dehydrogenase [NADP]
KeywordsOXIDOREDUCTASE / Trypanosoma cruzi / metabolism / isocitrate dehydrogenase
Function / homology
Function and homology information


isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / tricarboxylic acid cycle / NAD binding / magnesium ion binding
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
ISOCITRIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Isocitrate dehydrogenase [NADP]
Similarity search - Component
Biological speciesTrypanosoma cruzi (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 / pdbx_struct_conn_angle / struct_conn
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_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.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_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.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

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Assembly

Deposited unit
A: Isocitrate dehydrogenase [NADP]
B: Isocitrate dehydrogenase [NADP]
C: Isocitrate dehydrogenase [NADP]
D: Isocitrate dehydrogenase [NADP]
E: Isocitrate dehydrogenase [NADP]
F: Isocitrate dehydrogenase [NADP]
G: Isocitrate dehydrogenase [NADP]
H: Isocitrate dehydrogenase [NADP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)382,85832
Polymers375,0538
Non-polymers7,80524
Water2,180121
1
A: Isocitrate dehydrogenase [NADP]
B: Isocitrate dehydrogenase [NADP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,7148
Polymers93,7632
Non-polymers1,9516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11720 Å2
ΔGint-81 kcal/mol
Surface area30980 Å2
MethodPISA
2
C: Isocitrate dehydrogenase [NADP]
D: Isocitrate dehydrogenase [NADP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,7148
Polymers93,7632
Non-polymers1,9516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11760 Å2
ΔGint-79 kcal/mol
Surface area30590 Å2
MethodPISA
3
E: Isocitrate dehydrogenase [NADP]
F: Isocitrate dehydrogenase [NADP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,7148
Polymers93,7632
Non-polymers1,9516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11790 Å2
ΔGint-79 kcal/mol
Surface area30680 Å2
MethodPISA
4
G: Isocitrate dehydrogenase [NADP]
H: Isocitrate dehydrogenase [NADP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,7148
Polymers93,7632
Non-polymers1,9516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11790 Å2
ΔGint-79 kcal/mol
Surface area30510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.765, 123.485, 127.040
Angle α, β, γ (deg.)90.00, 105.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Isocitrate dehydrogenase [NADP]


Mass: 46881.633 Da / Num. of mol.: 8 / Mutation: M1S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / Gene: Tc00.1047053506925.319 / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli)
References: UniProt: Q4E4L7, 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.: 8 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-ICT / ISOCITRIC ACID / Isocitric acid


Mass: 192.124 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.49 Å3/Da / Density % sol: 50.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 20% PEG 8000, 100mM imidazole/HCl pH6.5, 3% MPD

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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 14, 2017
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: 126184 / % possible obs: 86.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 8
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 0.734 / Mean I/σ(I) obs: 1.02 / % possible all: 88.5

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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: 0.929 / Cor.coef. Fo:Fc free: 0.861 / SU B: 11.252 / SU ML: 0.263 / Cross valid method: THROUGHOUT / ESU R Free: 0.383 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.283 5493 5 %RANDOM
Rwork0.202 ---
obs0.206 104805 76.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å20 Å2-0.91 Å2
2---1.17 Å20 Å2
3---2.18 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26288 0 496 121 26905
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01927424
X-RAY DIFFRACTIONr_bond_other_d0.0020.0225920
X-RAY DIFFRACTIONr_angle_refined_deg1.6571.96637040
X-RAY DIFFRACTIONr_angle_other_deg1.014359736
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.30553296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.45223.8961232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.369154888
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.52715160
X-RAY DIFFRACTIONr_chiral_restr0.0940.23992
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0230488
X-RAY DIFFRACTIONr_gen_planes_other0.0020.026352
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_it2.1713.81213208
X-RAY DIFFRACTIONr_mcbond_other2.1713.81113207
X-RAY DIFFRACTIONr_mcangle_it3.475.70816496
X-RAY DIFFRACTIONr_mcangle_other3.475.70916497
X-RAY DIFFRACTIONr_scbond_it2.113.97614216
X-RAY DIFFRACTIONr_scbond_other2.1093.97614214
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3785.8620544
X-RAY DIFFRACTIONr_long_range_B_refined5.33429.67230932
X-RAY DIFFRACTIONr_long_range_B_other5.33429.67330931
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 298 -
Rwork0.243 5621 -
obs--57.01 %

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