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- PDB-1lwd: CRYSTAL STRUCTURE OF NADP-DEPENDENT ISOCITRATE DEHYDROGENASE FROM... -

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Basic information

Entry
Database: PDB / ID: 1lwd
TitleCRYSTAL STRUCTURE OF NADP-DEPENDENT ISOCITRATE DEHYDROGENASE FROM PORCINE HEART MITOCHONDRIA
ComponentsIsocitrate Dehydrogenase
KeywordsOXIDOREDUCTASE / TRICARBOXYLIC ACID CYCLE / NADP
Function / homology
Function and homology information


isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / NADP+ metabolic process / 2-oxoglutarate metabolic process / glyoxylate cycle / tricarboxylic acid cycle / 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
ISOCITRIC ACID / : / Isocitrate dehydrogenase [NADP], mitochondrial
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MAD / Resolution: 1.85 Å
AuthorsCeccarelli, C. / Bahnson, B.J.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal Structure of Porcine Mitochondrial NADP+-Dependent Isocitrate Dehydrogenase Complexed with Mn2+ and Isocitrate
Authors: Ceccarelli, C. / Grodsky, N.B. / Ariyaratne, N. / Colman, R.F. / Bahnson, B.J.
History
DepositionMay 31, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: 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
B: Isocitrate Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,0778
Polymers93,3902
Non-polymers6866
Water12,881715
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8440 Å2
ΔGint-83 kcal/mol
Surface area31820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.860, 112.569, 66.080
Angle α, β, γ (deg.)90.00, 97.00, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1058-

HOH

21B-1012-

HOH

31B-1033-

HOH

41B-1121-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.53688, 0.63102, 0.55998), (0.63108, -0.14013, 0.76295), (0.55991, 0.76301, -0.32299)
Vector: 7.36492, -37.67679, 36.53458)
DetailsTHE BIOLOGICALLY FUNCTIONAL MOLECULE IS A DIMER FORMED BY SUBUNITS A AND B, EACH OF WHICH IS PRESENT IN THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT

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Components

#1: Protein Isocitrate Dehydrogenase / Oxalosuccinate decarboxylase / IDH / NADP+-specific ICDH / IDP / ICD-M


Mass: 46695.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Organ: heart / Plasmid: PMALCIDP1 / Production host: Escherichia coli (E. coli) / Strain (production host): TB1
References: UniProt: P33198, isocitrate dehydrogenase (NADP+)
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-ICT / ISOCITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 715 / 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: 2.73 Å3/Da / Density % sol: 55 %
Description: THE STRUCTURE OF THE SE-MET CRYSTAL WAS SOLVED BY MULTIWAVELENGTH ANOMALOUS DIFFRACTION (MAD). THE THREE-WAVELENGTH MAD EXPERIMENT WAS PERFORMED ON BEAMLINE X12-C AT THE NSLS, BROOKHAVEN NATIONAL LABORATORY.
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: 20 MG/ML PROTEIN, 100 MM TRIETHANOLAMINE CHLORIDE PH 7.7, 150 MM SODIUM SULFATE, 8 MM ISOCITRATE, 4 MM MANGANESE SULFATE, 20% PEG 6000, 3% GLYCEROL, pH 7.70, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
20.1 MTEA-Cl1droppH7.7
30.15 M1dropNa2SO4
48 mMdl-isocitrate1drop
54 mM1dropMnSO4
620 %PEG60001drop
73 %glycerol1drop
80.1 MTEA-Cl1reservoirpH7.7
90.15 M1reservoirNa2SO4
1020 %PEG60001reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 1, 1999 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 88689 / Num. obs: 88689 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.767 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 11.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.643 % / Rmerge(I) obs: 0.963 / Mean I/σ(I) obs: 1.4 / Num. unique all: 8584 / % possible all: 92.7
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 30 Å / Num. measured all: 334110

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
RefinementMethod to determine structure: MAD
Starting model: ISOMORPHOUS SE-MET CRYSTAL STRUCTURE

Resolution: 1.85→29.23 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: NCS RESTRAINTS WERE APPLIED TO 3074 OF 3285 PAIRS OF ATOMS IN THE A AND B SUBUNITS OF THE PROTEIN. SEE REMARK 295 FOR RESIDUES AND SIDE CHAIN ATOMS OMITTED FROM NCS RESTRAINTS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21 7728 9.9 %RANDOM
Rwork0.182 ---
all0.198 82400 --
obs0.185 77739 91.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.6925 Å2 / ksol: 0.352708 e/Å3
Displacement parametersBiso mean: 27.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å2-0.26 Å2
2---1.01 Å20 Å2
3---2.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.85→29.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6570 0 38 715 7323
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.161.5
X-RAY DIFFRACTIONc_mcangle_it1.742
X-RAY DIFFRACTIONc_scbond_it2.032
X-RAY DIFFRACTIONc_scangle_it3.022.5
Refine LS restraints NCSNCS model details: RESTRAINED / Rms dev Biso : 1.936 Å2 / Rms dev position: 0.066 Å / Weight Biso : 2 / Weight position: 50
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.298 1153 10.1 %
Rwork0.277 10267 -
obs-10267 80.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4ISOCITRATE.PARAMISOCITRATE.TOP
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.25
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.57
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76

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