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- PDB-5h3f: Crystal structure of mouse isocitrate dehydrogenases 2 complexed ... -

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Basic information

Entry
Database: PDB / ID: 5h3f
TitleCrystal structure of mouse isocitrate dehydrogenases 2 complexed with isocitrate
ComponentsIsocitrate dehydrogenase [NADP], mitochondrial
KeywordsOXIDOREDUCTASE / NADP dependent isocitrate dehydrogenases 2
Function / homology
Function and homology information


Citric acid cycle (TCA cycle) / Maturation of TCA enzymes and regulation of TCA cycle / Transcriptional activation of mitochondrial biogenesis / negative regulation of glial cell migration / negative regulation of matrix metallopeptidase secretion / NADP+ biosynthetic process / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / 2-oxoglutarate metabolic process ...Citric acid cycle (TCA cycle) / Maturation of TCA enzymes and regulation of TCA cycle / Transcriptional activation of mitochondrial biogenesis / negative regulation of glial cell migration / negative regulation of matrix metallopeptidase secretion / NADP+ biosynthetic process / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / 2-oxoglutarate metabolic process / glyoxylate cycle / Mitochondrial protein degradation / negative regulation of glial cell proliferation / tricarboxylic acid cycle / NAD binding / peroxisome / 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: 3.29 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

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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)96,2166
Polymers95,7832
Non-polymers4334
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8150 Å2
ΔGint-76 kcal/mol
Surface area33780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.853, 135.853, 220.162
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 47891.543 Da / Num. of mol.: 2
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-ICT / ISOCITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 6.14 Å3/Da / Density % sol: 79.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M sodium tribasic dehydrate, 11.5%(v/v) 2-propanol, 10.8%(w/v) PEG4000

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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: Jun 15, 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: 3.29→45.9 Å / Num. obs: 35964 / % possible obs: 99.3 % / Redundancy: 10.4 % / Net I/σ(I): 14.1
Reflection shellResolution: 3.29→3.49 Å / Redundancy: 9.7 % / Mean I/σ(I) obs: 2.1 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
XDSdata scaling
MOLREPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LWD

1lwd


Resolution: 3.29→19.89 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 20.298 / SU ML: 0.294 / Cross valid method: THROUGHOUT / ESU R: 0.61 / ESU R Free: 0.33 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1789 5 %RANDOM
Rwork0.192 ---
obs0.194 33999 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 119.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20.2 Å20 Å2
2--0.4 Å20 Å2
3----1.29 Å2
Refinement stepCycle: LAST / Resolution: 3.29→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6604 0 28 4 6636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196778
X-RAY DIFFRACTIONr_bond_other_d0.0010.026457
X-RAY DIFFRACTIONr_angle_refined_deg1.0291.9469154
X-RAY DIFFRACTIONr_angle_other_deg0.839314882
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5565830
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.69424.221308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.226151198
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6281536
X-RAY DIFFRACTIONr_chiral_restr0.060.2998
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027628
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021572
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_it2.97411.8413326
X-RAY DIFFRACTIONr_mcbond_other2.96911.8393325
X-RAY DIFFRACTIONr_mcangle_it4.97217.764154
X-RAY DIFFRACTIONr_mcangle_other4.97317.7634155
X-RAY DIFFRACTIONr_scbond_it3.11112.2653452
X-RAY DIFFRACTIONr_scbond_other3.11212.2633450
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.49618.2225000
X-RAY DIFFRACTIONr_long_range_B_refined8.18192.2087292
X-RAY DIFFRACTIONr_long_range_B_other8.18192.2167293
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.29→3.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 119 -
Rwork0.387 2268 -
obs--92.95 %

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