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- PDB-3map: Crystal structure of homodimeric R132H mutant of human cytosolic ... -

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Basic information

Entry
Database: PDB / ID: 3map
TitleCrystal structure of homodimeric R132H mutant of human cytosolic NADP(+)-dependent isocitrate dehydrogenase in complex with NADP and isocitrate
ComponentsIsocitrate dehydrogenase [NADP] cytoplasmic
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 / 2-oxoglutarate metabolic process / 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 / 2-oxoglutarate metabolic process / NADP 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 / secretory granule lumen / ficolin-1-rich granule lumen / response to oxidative stress / cadherin binding / Neutrophil degranulation / magnesium ion binding / protein homodimerization activity / mitochondrion / extracellular exosome / extracellular region / identical protein binding / cytosol / cytoplasm
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: 2.8 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
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

Downloads & links

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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)97,4166
Polymers95,5452
Non-polymers1,8714
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-30 kcal/mol
Surface area33380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.836, 79.836, 295.956
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.: 2 / 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: 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
#3: Chemical ChemComp-ICT / ISOCITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7

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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: 2.52 Å3/Da / Density % sol: 51.28 % / Mosaicity: 0.45 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl, 2.0M (NH4)2SO4, pH 8.5, 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: May 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 24708 / % possible obs: 100 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.096 / Χ2: 1.031 / Net I/σ(I): 7.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.8-2.9130.67524010.6651100
2.9-3.0214.40.48324030.6941100
3.02-3.1514.60.31924150.721100
3.15-3.3214.60.21324330.761100
3.32-3.5314.40.14124170.8431100
3.53-3.814.20.10624590.991100
3.8-4.18140.09424531.317199.9
4.18-4.7913.50.10324631.834199.8
4.79-6.0313.80.08525281.5841100
6.03-5012.90.03327360.914199.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T09

1t09


Resolution: 2.8→39.918 Å / Occupancy max: 1 / Occupancy min: 0.9 / FOM work R set: 0.807 / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 0.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1183 5.04 %RANDOM
Rwork0.224 ---
obs0.227 23449 95.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.07 Å2 / ksol: 0.365 e/Å3
Displacement parametersBiso max: 161.87 Å2 / Biso mean: 69.421 Å2 / Biso min: 27.66 Å2
Baniso -1Baniso -2Baniso -3
1-2.849 Å20 Å2-0 Å2
2--2.849 Å20 Å2
3----5.698 Å2
Refinement stepCycle: LAST / Resolution: 2.8→39.918 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6255 0 122 0 6377
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046511
X-RAY DIFFRACTIONf_angle_d0.8528793
X-RAY DIFFRACTIONf_chiral_restr0.064963
X-RAY DIFFRACTIONf_plane_restr0.0121109
X-RAY DIFFRACTIONf_dihedral_angle_d20.552491
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.9280.3311380.2922540267889
2.928-3.0820.3041270.2582633276092
3.082-3.2750.3091710.2462629280094
3.275-3.5270.2811680.2282751291996
3.527-3.8820.271310.2222826295797
3.882-4.4430.2541440.1892862300698
4.443-5.5960.2371420.1792915305798
5.596-39.9220.2461620.2373110327298
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)
1-0.0257-0.1055-0.02880.7497-0.32180.54780.0172-0.0108-0.0256-0.0433-0.06590.03240.07890.0899-00.27440.0541-0.03420.3075-0.02810.2674-2.477532.299614.6486
20.05150.06980.02520.66360.5170.6481-0.0588-0.0259-0.0192-0.0216-0.04940.1261-0.0047-0.001500.2727-0.01270.01360.3171-0.00190.3487-8.716128.8667-17.8259
30.00160.0251-0.0107-0.01930.02640.0125-0.23870.0118-0.1098-0.0138-0.22820.1921-0.02150.192900.48770.0248-0.01570.5652-0.10330.4802-5.969525.1745-0.4219
40.0066-0.0012-0.04120.01330.00610.0726-0.0675-0.10250.04620.06760.001-0.0072-0.0512-0.0503-01.3363-0.01710.27641.19680.01751.4381-5.08735.4022-1.2218
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN AA3 - 413
2X-RAY DIFFRACTION2CHAIN BB3 - 413

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