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

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Basic information

Entry
Database: PDB / ID: 4ajs
Title3D structure of E. coli Isocitrate Dehydrogenase K100M mutant in complex with isocitrate, magnesium(II), Adenosine 2',5'-biphosphate and ribosylnicotinamide-5'-phosphate
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 / electron transport chain / tricarboxylic acid cycle / NAD binding / response to oxidative stress / magnesium ion binding / cytosol / cytoplasm
Similarity search - Function
Isocitrate dehydrogenase NADP-dependent, dimeric, prokaryotic / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isocitrate and isopropylmalate dehydrogenases signature. / Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-2'-5'-DIPHOSPHATE / ISOCITRIC ACID / BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / Isocitrate dehydrogenase [NADP]
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.802 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

Downloads & links

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Assembly

Deposited unit
A: ISOCITRATE DEHYDROGENASE [NADP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8866
Polymers45,8121
Non-polymers1,0755
Water9,080504
1
A: ISOCITRATE DEHYDROGENASE [NADP]
hetero molecules

A: ISOCITRATE DEHYDROGENASE [NADP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,77312
Polymers91,6232
Non-polymers2,15010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area10490 Å2
ΔGint-82.5 kcal/mol
Surface area31330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.585, 103.585, 149.680
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 / ISOCITRATE DEHYDROGENASE


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

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Non-polymers , 6 types, 509 molecules

#2: Chemical ChemComp-A2P / ADENOSINE-2'-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#3: Chemical ChemComp-ICT / ISOCITRIC ACID / 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: Chemical ChemComp-NMN / BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / NICOTINAMIDE MONONUCLEOTIDE / Nicotinamide mononucleotide


Mass: 335.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16N2O8P
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 504 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsRIBOSYLNICOTINAMIDE-5'-PHOSPHATE (NMN): NADP FRAGMENT FROM HYDROLYSIS ADENOSINE 2',5'-BIPHOSPHATE ...RIBOSYLNICOTINAMIDE-5'-PHOSPHATE (NMN): NADP FRAGMENT FROM HYDROLYSIS ADENOSINE 2',5'-BIPHOSPHATE (A2P): 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: ID23-1 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Details: TOROIDAL MIRROR
RadiationMonochromator: SILICON (1 1 1) CHANNEL- CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 75372 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 11.3 % / Biso Wilson estimate: 22.81 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 12.3
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.6 / % possible all: 98.5

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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: 1.802→46.325 Å / SU ML: 0.38 / σ(F): 1.99 / Phase error: 17.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1919 3768 5 %
Rwork0.169 --
obs0.1702 75365 99.69 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.152 Å2 / ksol: 0.378 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.6051 Å20 Å20 Å2
2---3.6051 Å20 Å2
3----12.1524 Å2
Refinement stepCycle: LAST / Resolution: 1.802→46.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3204 0 68 504 3776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073377
X-RAY DIFFRACTIONf_angle_d1.0414588
X-RAY DIFFRACTIONf_dihedral_angle_d13.6461285
X-RAY DIFFRACTIONf_chiral_restr0.072507
X-RAY DIFFRACTIONf_plane_restr0.004592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8024-1.86690.28363580.25266876X-RAY DIFFRACTION98
1.8669-1.94160.25323570.2117107X-RAY DIFFRACTION100
1.9416-2.030.20333650.18997115X-RAY DIFFRACTION100
2.03-2.1370.19593470.1777115X-RAY DIFFRACTION100
2.137-2.27090.19644080.17257062X-RAY DIFFRACTION100
2.2709-2.44620.20353890.16877114X-RAY DIFFRACTION100
2.4462-2.69240.20123680.17537190X-RAY DIFFRACTION100
2.6924-3.08190.20083840.1737207X-RAY DIFFRACTION100
3.0819-3.88260.18513950.15267244X-RAY DIFFRACTION100
3.8826-46.33990.16153970.15367567X-RAY DIFFRACTION100

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