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- PDB-2qfx: Crystal structure of Saccharomyces cerevesiae mitochondrial NADP(... -

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Basic information

Entry
Database: PDB / ID: 2qfx
TitleCrystal structure of Saccharomyces cerevesiae mitochondrial NADP(+)-dependent isocitrate dehydrogenase in complex with NADPH, a-ketoglutarate and Ca(2+)
ComponentsIsocitrate dehydrogenase [NADP]
KeywordsOXIDOREDUCTASE / Rossmann fold
Function / homology
Function and homology information


NADPH regeneration / Peroxisomal protein import / isocitrate metabolic process / : / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / NADP+ metabolic process / glyoxylate cycle / mitochondrial nucleoid / tricarboxylic acid cycle ...NADPH regeneration / Peroxisomal protein import / isocitrate metabolic process / : / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / NADP+ metabolic process / glyoxylate cycle / mitochondrial nucleoid / tricarboxylic acid cycle / Neutrophil degranulation / NAD binding / magnesium ion binding / mitochondrion
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
2-OXOGLUTARIC ACID / Chem-NDP / Isocitrate dehydrogenase [NADP], mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPeng, Y.J. / Ding, J.P.
CitationJournal: Protein Sci. / Year: 2008
Title: Structural studies of Saccharomyces cerevesiae mitochondrial NADP-dependent isocitrate dehydrogenase in different enzymatic states reveal substantial conformational changes during the catalytic reaction
Authors: Peng, Y.J. / Zhong, C. / Huang, W. / Ding, J.P.
History
DepositionJun 28, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Oct 25, 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 / 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 1.4Nov 15, 2023Group: Advisory / Other / Category: pdbx_validate_symm_contact / symmetry
Item: _symmetry.Int_Tables_number / _symmetry.space_group_name_H-M

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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]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)294,44824
Polymers288,8596
Non-polymers5,59018
Water4,089227
1
A: Isocitrate dehydrogenase [NADP]
B: Isocitrate dehydrogenase [NADP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,1498
Polymers96,2862
Non-polymers1,8636
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11510 Å2
ΔGint-76 kcal/mol
Surface area30760 Å2
MethodPISA
2
C: Isocitrate dehydrogenase [NADP]
D: Isocitrate dehydrogenase [NADP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,1498
Polymers96,2862
Non-polymers1,8636
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11510 Å2
ΔGint-75 kcal/mol
Surface area30640 Å2
MethodPISA
3
E: Isocitrate dehydrogenase [NADP]
F: Isocitrate dehydrogenase [NADP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,1498
Polymers96,2862
Non-polymers1,8636
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11600 Å2
ΔGint-76 kcal/mol
Surface area30560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.415, 99.630, 129.950
Angle α, β, γ (deg.)90.00, 111.21, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein
Isocitrate dehydrogenase [NADP] / Idp1p / Oxalosuccinate decarboxylase / IDH / NADP+ / -specific ICDH / IDP


Mass: 48143.086 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: YPH499 / Gene: IDP1 / Plasmid: pET-3E-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS
References: UniProt: P21954, isocitrate dehydrogenase (NADP+)
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H6O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.37 Å3/Da / Density % sol: 48.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 100mM Tris-HCl, 25% PEG 4000, 0.2M Na-acetate, 4% 1,3-propanediol, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 17, 2006 / Details: mirrors
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 73998 / % possible obs: 98.6 % / Redundancy: 5.2 % / Biso Wilson estimate: 76 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.037 / Χ2: 1.086 / Net I/σ(I): 15
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.2 / Num. unique all: 7276 / Rsym value: 0.341 / Χ2: 1.017 / % possible all: 97.6

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Phasing

Phasing MRCor.coef. Fo:Fc: 0.322 / Packing: 0.592
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Translation4 Å10 Ågeneral98.8 2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QFW

2qfw


Resolution: 2.7→49.73 Å / Rfactor Rfree error: 0.005 / FOM work R set: 0.744 / Data cutoff high absF: 1808941.125 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.285 3717 5.1 %RANDOM
Rwork0.217 ---
obs-73241 98.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.325 Å2 / ksol: 0.318 e/Å3
Displacement parametersBiso mean: 68.9 Å2
Baniso -1Baniso -2Baniso -3
1--15.54 Å20 Å2-11.51 Å2
2--21.83 Å20 Å2
3----6.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.7→49.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19488 0 354 227 20069
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.7-2.720.359760.36713251401
2.72-2.740.551750.40113441419
2.74-2.760.427700.37514301500
2.76-2.780.415690.3913531422
2.78-2.80.433660.37113631429
2.8-2.820.398640.35913801444
2.82-2.840.379800.34913901470
2.84-2.860.411810.37813431424
2.86-2.880.512870.36413741461
2.88-2.910.385760.3713781454
2.91-2.930.453760.32913561432
2.93-2.960.482690.34913651434
2.96-2.990.328620.30814261488
2.99-3.010.395810.32813361417
3.01-3.040.414760.32613711447
3.04-3.070.337620.27214151477
3.07-3.10.399760.29414021478
3.1-3.130.355680.2813801448
3.13-3.170.33790.28213731452
3.17-3.20.339630.26413981461
3.2-3.240.341810.25413811462
3.24-3.280.317740.27714051479
3.28-3.320.408730.26213911464
3.32-3.360.336710.27714201491
3.36-3.40.393820.28413741456
3.4-3.450.363930.28213821475
3.45-3.50.297800.26113831463
3.5-3.550.325810.25814341515
3.55-3.610.299630.21513791442
3.61-3.660.32660.2214471513
3.66-3.730.292860.21313821468
3.73-3.80.293820.22414201502
3.8-3.870.243760.19514141490
3.87-3.950.259650.19713991464
3.95-4.030.266590.19214241483
4.03-4.130.255690.213861455
4.13-4.230.275780.19214211499
4.23-4.340.245740.16914261500
4.34-4.470.217740.16613811455
4.47-4.620.22900.16413821472
4.62-4.780.212800.16613951475
4.78-4.970.237840.16114161500
4.97-5.20.245680.18113961464
5.2-5.470.278620.19214271489
5.47-5.810.279670.20414351502
5.81-6.260.301800.19814291509
6.26-6.890.228750.18114041479
6.89-7.880.204660.15214271493
7.88-9.920.25830.17114001483
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3NDP.paramNDP.top
X-RAY DIFFRACTION4AKG.paramAKG.top
X-RAY DIFFRACTION5ion.paramion.top

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