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- PDB-4aov: DpIDH-NADP. The complex structures of Isocitrate dehydrogenase fr... -

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Basic information

Entry
Database: PDB / ID: 4aov
TitleDpIDH-NADP. The complex structures of Isocitrate dehydrogenase from Clostridium thermocellum and Desulfotalea psychrophila, support a new active site locking mechanism
ComponentsISOCITRATE DEHYDROGENASE [NADP]
KeywordsOXIDOREDUCTASE / TEMPERATURE ADAPTATION / THERMOPHILIC / PSYCHROPHILIC / NADP+ SELECTIVITY / DOMAIN MOVEMENTS
Function / homology
Function and homology information


isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / NADP metabolic process / tricarboxylic acid cycle / peroxisome / NAD binding / magnesium ion binding / cytosol
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]
Similarity search - Component
Biological speciesDESULFOTALEA PSYCHROPHILA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsLeiros, H.-K.S. / Fedoy, A.-E. / Leiros, I. / Steen, I.H.
CitationJournal: FEBS Open Bio. / Year: 2012
Title: The Complex Structures of Isocitrate Dehydrogenase from Clostridium Thermocellum and Desulfotalea Psychrophila Suggest a New Active Site Locking Mechanism
Authors: Leiros, H.-K.S. / Fedoy, A.-E. / Leiros, I. / Steen, I.H.
History
DepositionMar 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Database references
Revision 1.2May 22, 2013Group: Database references
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6094
Polymers45,6491
Non-polymers9603
Water4,089227
1
A: ISOCITRATE DEHYDROGENASE [NADP]
hetero molecules

A: ISOCITRATE DEHYDROGENASE [NADP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,2188
Polymers91,2982
Non-polymers1,9206
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area12100 Å2
ΔGint-64.8 kcal/mol
Surface area29040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.640, 98.910, 71.890
Angle α, β, γ (deg.)90.00, 103.94, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2128-

HOH

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Components

#1: Protein ISOCITRATE DEHYDROGENASE [NADP]


Mass: 45649.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DESULFOTALEA PSYCHROPHILA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): EB106
References: UniProt: Q6AQ66, isocitrate dehydrogenase (NADP+)
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-ICT / ISOCITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#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: 2.33 Å3/Da / Density % sol: 47.2 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop
Details: HANGING DROP METHOD. RESERVOIR SOLUTIONS WITH 100 MM TRIS/HCL BUFFER AT PH 7.4, 1.7-1.9 M AMMONIUM SULFATE, 2% PEG 400 AND 60 MM MAGNESIUM SULFATE. PROTEIN SOLUTION: 20 MG/ML DPIDH, 10 MM ...Details: HANGING DROP METHOD. RESERVOIR SOLUTIONS WITH 100 MM TRIS/HCL BUFFER AT PH 7.4, 1.7-1.9 M AMMONIUM SULFATE, 2% PEG 400 AND 60 MM MAGNESIUM SULFATE. PROTEIN SOLUTION: 20 MG/ML DPIDH, 10 MM NADP AND 10 MM DL-ISOCITRATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.8536
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8536 Å / Relative weight: 1
ReflectionResolution: 1.93→40 Å / Num. obs: 30844 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.7
Reflection shellResolution: 1.93→2.03 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.7 / % possible all: 98.1

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Processing

SoftwareName: REFMAC / Version: 5.3.0021 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.883 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22542 1563 5.1 %RANDOM
Rwork0.1749 ---
obs0.17745 29252 98.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.858 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20.52 Å2
2--0.05 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.93→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3180 0 62 227 3469
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223360
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.9784558
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1895411
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.95624.503151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.28215580
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1991518
X-RAY DIFFRACTIONr_chiral_restr0.0990.2500
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022528
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.21555
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22327
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2238
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.2126
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.240
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.71.52102
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0923279
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.71531468
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4954.51279
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 104 -
Rwork0.234 1830 -
obs--85.2 %

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