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- PDB-3mas: Crystal structure of heterodimeric R132H mutant of human cytosoli... -

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Basic information

Entry
Database: PDB / ID: 3mas
TitleCrystal structure of heterodimeric R132H mutant of human cytosolic NADP(+)-dependent isocitrate dehydrogenase in complex with NADP and isocitrate
Components(Isocitrate dehydrogenase [NADP] cytoplasmic) x 2
KeywordsOXIDOREDUCTASE / isocitrate dehydrogenase / nicotinamide adenine dinucleotide phosphate / Rossmann fold
Function / homology
Function and homology information


Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate / NADPH regeneration / regulation of phospholipid catabolic process / regulation of phospholipid biosynthetic process / NFE2L2 regulating TCA cycle genes / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / NADPH regeneration / NADP+ metabolic process ...Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate / NADPH regeneration / regulation of phospholipid catabolic process / regulation of phospholipid biosynthetic process / NFE2L2 regulating TCA cycle genes / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / NADPH regeneration / NADP+ metabolic process / 2-oxoglutarate metabolic process / glyoxylate cycle / response to steroid hormone / female gonad development / peroxisomal matrix / tricarboxylic acid cycle / glutathione metabolic process / Peroxisomal protein import / NAD binding / peroxisome / tertiary granule lumen / NADP binding / response to oxidative stress / secretory granule lumen / ficolin-1-rich granule lumen / cadherin binding / Neutrophil degranulation / magnesium ion binding / protein homodimerization activity / mitochondrion / extracellular exosome / extracellular region / identical protein binding / cytoplasm / 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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Isocitrate dehydrogenase [NADP] cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsYang, B. / Peng, Y. / Ding, J.
CitationJournal: Cell Res. / Year: 2010
Title: Molecular mechanisms of "off-on switch" of activities of human IDH1 by tumor-associated mutation R132H.
Authors: Yang, B. / Zhong, C. / Peng, Y. / Lai, Z. / Ding, J.
History
DepositionMar 24, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 21, 2014Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 1, 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] cytoplasmic
B: Isocitrate dehydrogenase [NADP] cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8816
Polymers95,0102
Non-polymers1,8714
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-29 kcal/mol
Surface area36210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.136, 83.136, 308.508
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Isocitrate dehydrogenase [NADP] cytoplasmic / IDH / Cytosolic NADP-isocitrate dehydrogenase / Oxalosuccinate decarboxylase / NADP(+)-specific ICDH / IDP


Mass: 47772.316 Da / Num. of mol.: 1 / Mutation: R132H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IDH1, PICD / Plasmid: pRSF-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O75874, isocitrate dehydrogenase (NADP+)
#2: Protein Isocitrate dehydrogenase [NADP] cytoplasmic / IDH / Cytosolic NADP-isocitrate dehydrogenase / Oxalosuccinate decarboxylase / NADP(+)-specific ICDH / IDP


Mass: 47237.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IDH1, PICD / Plasmid: pGEX-4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O75874, isocitrate dehydrogenase (NADP+)
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-ICT / ISOCITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
Sequence detailsTHE PROTEIN IS A HETERODIMERIC MUTANT, WITH ARG 132 MUTATED TO HIS 132 IN ONE SUBUNIT, WHILE THE ...THE PROTEIN IS A HETERODIMERIC MUTANT, WITH ARG 132 MUTATED TO HIS 132 IN ONE SUBUNIT, WHILE THE ARG132 IN THE OTHER SUBUNIT REMAINED THE SAME AS WILD TYPE PROTEIN

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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: 2.85 Å3/Da / Density % sol: 56.89 % / Mosaicity: 0.534 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES-Na, 2% PEG 400, 2.0M (NH4)2SO4, pH 7.5, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 18264 / % possible obs: 96.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.114 / Χ2: 0.735 / Net I/σ(I): 5.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.2-3.317.80.59618190.439199.9
3.31-3.4580.40818320.432199.8
3.45-3.680.27918350.474199.8
3.6-3.797.90.20118580.544199.8
3.79-4.037.60.15718160.686199.3
4.03-4.347.20.13118000.985196.5
4.34-4.786.70.10617461.268193.2
4.78-5.476.50.08418011.089194.3
5.47-6.896.80.05918840.753196.9
6.89-5050.03318731.015189.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T09

1t09


Resolution: 3.2→49.547 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.786 / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.283 871 5.08 %RANDOM
Rwork0.233 ---
obs0.235 17148 91.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.647 Å2 / ksol: 0.339 e/Å3
Displacement parametersBiso max: 125.46 Å2 / Biso mean: 85.832 Å2 / Biso min: 67.14 Å2
Baniso -1Baniso -2Baniso -3
1--1.644 Å2-0 Å20 Å2
2---1.644 Å2-0 Å2
3---3.287 Å2
Refinement stepCycle: LAST / Resolution: 3.2→49.547 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6235 0 122 0 6357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046491
X-RAY DIFFRACTIONf_angle_d0.7568762
X-RAY DIFFRACTIONf_chiral_restr0.057957
X-RAY DIFFRACTIONf_plane_restr0.0121103
X-RAY DIFFRACTIONf_dihedral_angle_d19.7442499
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.4010.3481550.3042521267688
3.401-3.6630.3181370.2652655279291
3.663-4.0320.2991410.2322757289894
4.032-4.6150.2511450.2022707285291
4.615-5.8130.2531430.1992753289692
5.813-49.5530.2731500.2262884303490

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