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- PDB-4ajr: 3D structure of E. coli Isocitrate Dehydrogenase K100M mutant in ... -

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Basic information

Entry
Database: PDB / ID: 4ajr
Title3D structure of E. coli Isocitrate Dehydrogenase K100M mutant in complex with alpha-ketoglutarate, magnesium(II) and NADPH - The product complex
ComponentsISOCITRATE DEHYDROGENASE [NADP]
KeywordsOXIDOREDUCTASE / OXIDATIVE BETA-DECARBOXYLATION
Function / homology
Function and homology information


isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / glyoxylate cycle / guanosine tetraphosphate binding / tricarboxylic acid cycle / electron transport chain / NAD binding / response to oxidative stress / magnesium ion binding / cytoplasm / cytosol
Similarity search - Function
Isocitrate dehydrogenase NADP-dependent, dimeric, prokaryotic / 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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / Isocitrate dehydrogenase [NADP]
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.687 Å
AuthorsGoncalves, S. / Miller, S.P. / Carrondo, M.A. / Dean, A.M. / Matias, P.M.
CitationJournal: Biochemistry / Year: 2012
Title: Induced Fit and the Catalytic Mechanism of Isocitrate Dehydrogenase.
Authors: Goncalves, S. / Miller, S.P. / Carrondo, M.A. / Dean, A.M. / Matias, P.M.
History
DepositionFeb 17, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: ISOCITRATE DEHYDROGENASE [NADP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0615
Polymers45,8121
Non-polymers1,2494
Water2,288127
1
A: ISOCITRATE DEHYDROGENASE [NADP]
hetero molecules

A: ISOCITRATE DEHYDROGENASE [NADP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,12110
Polymers91,6232
Non-polymers2,4988
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area12200 Å2
ΔGint-62.7 kcal/mol
Surface area29660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.788, 105.788, 145.488
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ISOCITRATE DEHYDROGENASE [NADP] / IDH / IDP / NADP(+)-SPECIFIC ICDH / OXALOSUCCINATE DECARBOXYLASE


Mass: 45811.578 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P08200, isocitrate dehydrogenase (NADP+)

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Non-polymers , 5 types, 131 molecules

#2: Chemical ChemComp-NMN / BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / NICOTINAMIDE MONONUCLEOTIDE


Mass: 335.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16N2O8P
#3: 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
#4: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 100 TO MET
Nonpolymer detailsNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NAP): THIS IS NADPH, THE REDUCED FORM OF NADP ...NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NAP): THIS IS NADPH, THE REDUCED FORM OF NADP RIBOSYLNICOTINAMIDE-5'-PHOSPHATE (NMP): THIS IS A NADP FRAGMENT FROM HYDROLYSIS

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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: 4.5 Å3/Da / Density % sol: 72 % / Description: NONE
Crystal growDetails: 1.85 M NH4SO4, 50 MM CITRIC ACID/NA2HPO4 BUFFER PH 5.2, 0.1 M NACL AND 0.2 M DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9535
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Details: TOROIDAL MIRROR
RadiationMonochromator: CHANNEL-CUT ESRF MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9535 Å / Relative weight: 1
ReflectionResolution: 2.69→60 Å / Num. obs: 23556 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Biso Wilson estimate: 47.08 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 15.2
Reflection shellResolution: 2.69→2.85 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 2.8 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AI2

1ai2


Resolution: 2.687→52.894 Å / SU ML: 0.66 / σ(F): 1.99 / Phase error: 18.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2091 1195 5.1 %
Rwork0.1604 --
obs0.1628 23554 99.51 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.034 Å2 / ksol: 0.396 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-22.8121 Å20 Å20 Å2
2--22.8121 Å20 Å2
3---13.9255 Å2
Refinement stepCycle: LAST / Resolution: 2.687→52.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3204 0 81 127 3412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083349
X-RAY DIFFRACTIONf_angle_d1.1394543
X-RAY DIFFRACTIONf_dihedral_angle_d17.2881264
X-RAY DIFFRACTIONf_chiral_restr0.069503
X-RAY DIFFRACTIONf_plane_restr0.004582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6873-2.79490.29211190.22692362X-RAY DIFFRACTION96
2.7949-2.92210.25221400.20132429X-RAY DIFFRACTION100
2.9221-3.07620.24931220.19192450X-RAY DIFFRACTION100
3.0762-3.26890.24631390.17022463X-RAY DIFFRACTION100
3.2689-3.52120.21551270.15422483X-RAY DIFFRACTION100
3.5212-3.87550.18991400.14312461X-RAY DIFFRACTION100
3.8755-4.4360.18151410.13112502X-RAY DIFFRACTION100
4.436-5.58790.18461350.13792523X-RAY DIFFRACTION100
5.5879-52.90420.20071320.17542686X-RAY DIFFRACTION100

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