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

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Basic information

Entry
Database: PDB / ID: 4ajb
Title3D structure of E. coli Isocitrate Dehydrogenase K100M mutant in complex with Isocitrate, magnesium(II) and thioNADP
ComponentsNADP ISOCITRATE DEHYDROGENASE
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
ISOCITRIC ACID / 7-THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Isocitrate dehydrogenase [NADP]
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 16, 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: NADP ISOCITRATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8845
Polymers45,8121
Non-polymers1,0724
Water8,827490
1
A: NADP ISOCITRATE DEHYDROGENASE
hetero molecules

A: NADP ISOCITRATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,76710
Polymers91,6232
Non-polymers2,1448
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area10690 Å2
ΔGint-82.6 kcal/mol
Surface area30960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.054, 103.054, 150.339
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 NADP 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) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P08200, isocitrate dehydrogenase (NADP+)

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Non-polymers , 5 types, 494 molecules

#2: Chemical ChemComp-TAP / 7-THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / TATP


Mass: 759.471 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O16P3S
#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: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 490 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 100 TO MET

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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: 1.85M 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: SLS / Beamline: X06DA / Wavelength: 0.9792
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Details: MIRRORS
RadiationMonochromator: BARTELS MONOCHROMATOR WITH DUAL CHANNEL CUT CRYSTALS
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→48.8 Å / Num. obs: 64372 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.2
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.2 / % possible all: 96.1

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Processing

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

1ai2


Resolution: 1.9→48.744 Å / SU ML: 0.42 / σ(F): 1.99 / Phase error: 16.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1805 3235 5 %
Rwork0.1663 --
obs0.1671 64286 99.89 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.608 Å2 / ksol: 0.378 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.1201 Å20 Å20 Å2
2---1.1201 Å20 Å2
3----9.8262 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.744 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3204 0 67 490 3761
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073390
X-RAY DIFFRACTIONf_angle_d1.0794612
X-RAY DIFFRACTIONf_dihedral_angle_d14.0021296
X-RAY DIFFRACTIONf_chiral_restr0.073510
X-RAY DIFFRACTIONf_plane_restr0.005596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.96790.26263080.24155951X-RAY DIFFRACTION99
1.9679-2.04670.22893060.20486026X-RAY DIFFRACTION100
2.0467-2.13990.1852910.1816069X-RAY DIFFRACTION100
2.1399-2.25270.183620.17115995X-RAY DIFFRACTION100
2.2527-2.39380.19573370.17166039X-RAY DIFFRACTION100
2.3938-2.57860.20613030.17366087X-RAY DIFFRACTION100
2.5786-2.83810.19863160.17356106X-RAY DIFFRACTION100
2.8381-3.24870.19073320.16846119X-RAY DIFFRACTION100
3.2487-4.09270.15353350.14476185X-RAY DIFFRACTION100
4.0927-48.75960.15493450.15216474X-RAY DIFFRACTION100

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