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- PDB-5kvu: Crystal structure of isocitrate dehydrogenase-2 in complex with N... -

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Basic information

Entry
Database: PDB / ID: 5kvu
TitleCrystal structure of isocitrate dehydrogenase-2 in complex with NADP(+) from Mycobacterium tuberculosis
ComponentsIsocitrate dehydrogenase
KeywordsOXIDOREDUCTASE / ICD / Structural Genomics / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / glyoxylate cycle / tricarboxylic acid cycle / peptidoglycan-based cell wall / magnesium ion binding / protein homodimerization activity / extracellular region / plasma membrane / cytosol
Similarity search - Function
Isocitrate dehydrogenase NADP-dependent, monomeric / Monomeric isocitrate dehydrogenase
Similarity search - Domain/homology
MALONIC ACID / D-MALATE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / SUCCINIC ACID / Isocitrate dehydrogenase [NADP] 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsCheng, Y.S. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: To Be Published
Title: Structural and kinetic characterization of isocitrate dehydrogenase-2 from Mycobacterium tuberculosis
Authors: Sacchettini, J.C. / Cheng, Y.S.
History
DepositionJul 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isocitrate dehydrogenase
B: Isocitrate dehydrogenase
C: Isocitrate dehydrogenase
D: Isocitrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)334,59420
Polymers330,6044
Non-polymers3,99116
Water7,620423
1
A: Isocitrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,5904
Polymers82,6511
Non-polymers9403
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Isocitrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6235
Polymers82,6511
Non-polymers9724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Isocitrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7296
Polymers82,6511
Non-polymers1,0785
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Isocitrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6535
Polymers82,6511
Non-polymers1,0024
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.827, 110.861, 114.914
Angle α, β, γ (deg.)86.010, 78.620, 76.790
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Isocitrate dehydrogenase / Probable isocitrate dehydrogenase [NADP] Icd2 (Oxalosuccinate decarboxylase) (IDH) (NADP+-specific ICDH) (IDP)


Mass: 82650.906 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: icd2, Rv0066c, LH57_00380 / Production host: Escherichia coli (E. coli)
References: UniProt: O53611, isocitrate dehydrogenase (NADP+)

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Non-polymers , 7 types, 439 molecules

#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: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O4
#6: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.75 Å3/Da / Density % sol: 55.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 8-10% Tacsimate and 18-20% (w/v) PEG 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0723 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.66→50 Å / Num. obs: 99474 / % possible obs: 98.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 35.89 Å2 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.067 / Rrim(I) all: 0.133 / Χ2: 2.136 / Net I/av σ(I): 18.377 / Net I/σ(I): 10.5 / Num. measured all: 390141
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.67-2.723.90.59648920.820.3470.691.34398
2.72-2.773.90.52949740.8510.3070.6111.34198.1
2.77-2.8240.45749260.8860.2650.5281.36298.1
2.82-2.8840.40849450.9040.2360.4721.41298.2
2.88-2.9440.36149210.9150.2090.4171.41898.2
2.94-3.0140.28750120.9440.1660.3321.46798.4
3.01-3.0840.2649610.9520.1510.31.52498.4
3.08-3.1740.22749270.9640.1310.2621.68198.4
3.17-3.2640.19549750.9680.1130.2261.798.6
3.26-3.3640.15549760.9770.090.181.88698.7
3.36-3.483.90.13849700.9820.080.1592.14598.7
3.48-3.623.90.11449720.9870.0660.1322.24998.8
3.62-3.793.90.1149990.9860.0640.1272.58998.9
3.79-3.993.90.09149910.990.0540.1062.74699.1
3.99-4.243.90.07649970.9930.0450.0882.80299.1
4.24-4.563.90.06649680.9950.0390.0773.03799.2
4.56-5.023.90.06250530.9950.0360.0723.01499.4
5.02-5.753.90.06750010.9940.040.0783.08399.5
5.75-7.243.90.06249840.9950.0360.0722.99499.5
7.24-503.80.04250300.9980.0250.0493.05899.5

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-3000data collection
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1j1w

1j1w


Resolution: 2.66→48.503 Å / FOM work R set: 0.8258 / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 24.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.228 4964 4.99 %
Rwork0.1784 94479 -
obs0.1809 99443 98.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.22 Å2 / Biso mean: 53.6 Å2 / Biso min: 25.36 Å2
Refinement stepCycle: final / Resolution: 2.66→48.503 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22875 0 259 423 23557
Biso mean--48.21 44.15 -
Num. residues----2942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00523647
X-RAY DIFFRACTIONf_angle_d0.92332046
X-RAY DIFFRACTIONf_chiral_restr0.0583573
X-RAY DIFFRACTIONf_plane_restr0.0044168
X-RAY DIFFRACTIONf_dihedral_angle_d13.7928892
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6601-2.69040.33361350.26812718285386
2.6904-2.7220.31311550.25013143329898
2.722-2.75520.32081600.2353182334298
2.7552-2.79010.3111740.23253129330398
2.7901-2.82680.27071540.2273148330298
2.8268-2.86550.30161580.23273157331598
2.8655-2.90640.2941650.23243122328798
2.9064-2.94980.33931760.23183137331398
2.9498-2.99590.26051410.2163214335598
2.9959-3.0450.27811720.2113123329598
3.045-3.09750.26291630.2133170333398
3.0975-3.15380.26941630.21313167333098
3.1538-3.21450.28611710.22483130330199
3.2145-3.28010.27511730.21083200337399
3.2801-3.35140.26741650.19673120328599
3.3514-3.42930.2431740.19063166334099
3.4293-3.51510.24321420.17733178332099
3.5151-3.61010.21911600.17613191335199
3.6101-3.71630.23851650.1773159332499
3.7163-3.83620.21071760.17023186336299
3.8362-3.97320.20861570.16493168332599
3.9732-4.13220.21091890.1653163335299
4.1322-4.32020.20341640.14723130329499
4.3202-4.54780.2011570.14163213337099
4.5478-4.83250.16051690.13713201337099
4.8325-5.20520.19181670.14543153332099
5.2052-5.72830.22141800.16253217339799
5.7283-6.55540.19351910.16283146333799
6.5554-8.25260.16991810.153531913372100
8.2526-48.51120.1621670.13743157332499

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