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

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Basic information

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


NADPH regeneration / Peroxisomal protein import / isocitrate metabolic process / glutamate biosynthetic 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 / glutamate biosynthetic 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Isocitrate dehydrogenase [NADP], mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isocitrate dehydrogenase [NADP]
B: Isocitrate dehydrogenase [NADP]
C: Isocitrate dehydrogenase [NADP]
D: Isocitrate dehydrogenase [NADP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,5468
Polymers192,5724
Non-polymers2,9744
Water17,114950
1
A: Isocitrate dehydrogenase [NADP]
B: Isocitrate dehydrogenase [NADP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,7734
Polymers96,2862
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8460 Å2
ΔGint-52 kcal/mol
Surface area32830 Å2
MethodPISA
2
C: Isocitrate dehydrogenase [NADP]
D: Isocitrate dehydrogenase [NADP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,7734
Polymers96,2862
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8470 Å2
ΔGint-57 kcal/mol
Surface area32820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.180, 71.440, 101.630
Angle α, β, γ (deg.)87.800, 88.000, 90.100
Int Tables number1
Space group name H-MP1

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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.: 4
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-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 950 / 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: 2.19 Å3/Da / Density % sol: 43.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 100mM MES, 25% PEG 1500, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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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 20, 2005 / 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: 2.2→50 Å / Num. obs: 78839 / % possible obs: 95.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 31.9 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.08 / Χ2: 1.055 / Net I/σ(I): 9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 3.9 / Num. unique all: 7647 / Rsym value: 0.226 / Χ2: 1.175 / % possible all: 92.9

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Phasing

Phasing MRCor.coef. Fo:Fc: 0.306 / Packing: 0.644
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Translation4 Å10 Ågeneral98 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: PDB ENTRY 1T09

1t09


Resolution: 2.3→45.15 Å / Rfactor Rfree error: 0.004 / FOM work R set: 0.821 / Data cutoff high absF: 1430788 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.258 3501 5 %RANDOM
Rwork0.198 ---
obs-69329 95.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.301 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 32.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å20.23 Å2-1.61 Å2
2---0.25 Å21.38 Å2
3---1.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.3→45.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12958 0 192 950 14100
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0.84
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
2.3-2.320.305720.25612521324
2.32-2.330.362720.24712591331
2.33-2.350.269710.22912931364
2.35-2.360.361550.2513101365
2.36-2.380.277820.21912591341
2.38-2.40.325620.23712691331
2.4-2.420.353710.24113361407
2.42-2.440.314590.19712361295
2.44-2.460.308760.22212631339
2.46-2.480.307840.23613171401
2.48-2.50.328710.24112341305
2.5-2.520.282780.23312611339
2.52-2.540.304580.21812901348
2.54-2.570.286710.20512901361
2.57-2.590.317550.22212601315
2.59-2.620.272760.22413221398
2.62-2.640.31600.21513041364
2.64-2.670.368610.26112661327
2.67-2.70.379710.2613201391
2.7-2.730.304680.22712781346
2.73-2.760.303800.22313121392
2.76-2.790.259550.22712991354
2.79-2.820.313680.23513041372
2.82-2.860.296620.2213421404
2.86-2.90.338640.2313281392
2.9-2.940.292690.22212531322
2.94-2.980.347690.2313851454
2.98-3.020.227800.19213091389
3.02-3.070.354680.21913321400
3.07-3.120.297650.2313381403
3.12-3.180.252770.19313571434
3.18-3.230.278700.20513431413
3.23-3.30.282600.21213691429
3.3-3.360.276650.2113351400
3.36-3.440.27760.20713721448
3.44-3.520.235820.20613411423
3.52-3.60.246620.18413591421
3.6-3.70.228690.18913561425
3.7-3.810.213790.18113491428
3.81-3.930.238600.18613601420
3.93-4.070.232770.18213201397
4.07-4.240.21920.15813471439
4.24-4.430.192890.15213451434
4.43-4.660.198630.15413341397
4.66-4.950.197830.1513531436
4.95-5.340.227790.16913581437
5.34-5.870.243720.19413541426
5.87-6.720.311640.21213531417
6.72-8.460.218770.16613581435
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3nadp.paramnadp.top

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