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- PDB-5h3e: Crystal structure of mouse isocitrate dehydrogenases 2 K256Q muta... -

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Basic information

Entry
Database: PDB / ID: 5h3e
TitleCrystal structure of mouse isocitrate dehydrogenases 2 K256Q mutant complexed with isocitrate
ComponentsIsocitrate dehydrogenase [NADP], mitochondrial
KeywordsOXIDOREDUCTASE / NADP dependent isocitrate dehydrogenases 2
Function / homology
Function and homology information


negative regulation of glial cell migration / negative regulation of matrix metallopeptidase secretion / Transcriptional activation of mitochondrial biogenesis / Citric acid cycle (TCA cycle) / NADP biosynthetic process / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / 2-oxoglutarate metabolic process / NADP metabolic process ...negative regulation of glial cell migration / negative regulation of matrix metallopeptidase secretion / Transcriptional activation of mitochondrial biogenesis / Citric acid cycle (TCA cycle) / NADP biosynthetic process / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / 2-oxoglutarate metabolic process / NADP metabolic process / glyoxylate cycle / negative regulation of glial cell proliferation / tricarboxylic acid cycle / peroxisome / NAD binding / mitochondrial inner membrane / magnesium ion binding / mitochondrion / cytosol
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 / Isocitrate dehydrogenase [NADP], mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsXu, Y. / Liu, L. / Miyakawa, T. / Nakamura, A. / Tanokura, M.
CitationJournal: Sci Rep / Year: 2017
Title: Studies on the regulatory mechanism of isocitrate dehydrogenase 2 using acetylation mimics
Authors: Xu, Y. / Liu, L. / Nakamura, A. / Someya, S. / Miyakawa, T. / Tanokura, M.
History
DepositionOct 23, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Nov 8, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)96,2146
Polymers95,7812
Non-polymers4334
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8630 Å2
ΔGint-67 kcal/mol
Surface area31950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.150, 58.150, 206.915
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Isocitrate dehydrogenase [NADP], mitochondrial / Isocitrate dehydrogenase 2


Mass: 47890.492 Da / Num. of mol.: 2 / Mutation: K256Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Idh2 / Organ: liver / Plasmid: pET-26b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): KRX
References: UniProt: P54071, isocitrate dehydrogenase (NADP+)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ICT / ISOCITRIC ACID / Isocitric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4 / Details: 0.1 M ammonium formate, 24%(w/v) PEG 3350

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 7, 2014
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.21→45.3 Å / Num. obs: 37204 / % possible obs: 94.5 % / Redundancy: 4.7 % / Net I/σ(I): 16
Reflection shellResolution: 2.21→2.34 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 3 / % possible all: 71.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
XDSdata scaling
MOLREPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L04

4l04


Resolution: 2.21→19.32 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.906 / SU B: 6.348 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.394 / ESU R Free: 0.236 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1874 4.9 %RANDOM
Rwork0.209 ---
obs0.211 36284 97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.21→19.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6507 0 28 128 6663
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196679
X-RAY DIFFRACTIONr_bond_other_d0.0010.026363
X-RAY DIFFRACTIONr_angle_refined_deg1.081.9469023
X-RAY DIFFRACTIONr_angle_other_deg0.847314667
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9775817
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.69624.211304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.622151180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7751536
X-RAY DIFFRACTIONr_chiral_restr0.0610.2985
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027517
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021551
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_it0.6413.1983274
X-RAY DIFFRACTIONr_mcbond_other0.6413.1973273
X-RAY DIFFRACTIONr_mcangle_it1.1284.7944089
X-RAY DIFFRACTIONr_mcangle_other1.1284.7954090
X-RAY DIFFRACTIONr_scbond_it0.533.2643405
X-RAY DIFFRACTIONr_scbond_other0.533.2643403
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.9424.8584934
X-RAY DIFFRACTIONr_long_range_B_refined2.50324.9727433
X-RAY DIFFRACTIONr_long_range_B_other2.49724.957423
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.21→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 119 -
Rwork0.225 2131 -
obs--78.62 %

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