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

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Basic information

Entry
Database: PDB / ID: 4ajc
Title3D structure of E. coli Isocitrate Dehydrogenase K100M mutant in complex with alpha-ketoglutarate, calcium(II) and adenine nucleotide phosphate
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
ADENOSINE-2'-5'-DIPHOSPHATE / 2-OXOGLUTARIC ACID / Isocitrate dehydrogenase [NADP] / Isocitrate dehydrogenase [NADP]
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.1Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.2Dec 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)46,5215
Polymers45,8121
Non-polymers7094
Water7,728429
1
A: NADP ISOCITRATE DEHYDROGENASE
hetero molecules

A: NADP ISOCITRATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,04210
Polymers91,6232
Non-polymers1,4198
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area9520 Å2
ΔGint-96.2 kcal/mol
Surface area31110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.715, 103.715, 149.577
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: Q1RD16, UniProt: P08200*PLUS, isocitrate dehydrogenase (NADP+)

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Non-polymers , 5 types, 433 molecules

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


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#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.: 429 / 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: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418
DetectorType: BRUKER AXS PT135 / Detector: CCD / Details: MONTEL MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→46.4 Å / Num. obs: 36981 / % possible obs: 100 % / Redundancy: 15.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 24.8
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

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

1ai2


Resolution: 2.3→44.302 Å / SU ML: 0.64 / σ(F): 0 / Phase error: 20.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.209 1822 5.1 %
Rwork0.1752 --
obs0.1769 36019 97.52 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.616 Å2 / ksol: 0.349 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.5443 Å20 Å20 Å2
2---1.5443 Å20 Å2
3----5.0273 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.302 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3204 0 43 429 3676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083354
X-RAY DIFFRACTIONf_angle_d1.1014555
X-RAY DIFFRACTIONf_dihedral_angle_d14.8961275
X-RAY DIFFRACTIONf_chiral_restr0.073502
X-RAY DIFFRACTIONf_plane_restr0.005592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.38220.27772030.2333324X-RAY DIFFRACTION98
2.3822-2.47760.30371760.22823340X-RAY DIFFRACTION97
2.4776-2.59030.26591640.21053346X-RAY DIFFRACTION97
2.5903-2.72690.26581720.2083360X-RAY DIFFRACTION97
2.7269-2.89770.23781880.19143325X-RAY DIFFRACTION97
2.8977-3.12140.231750.19193379X-RAY DIFFRACTION97
3.1214-3.43540.22461760.1743418X-RAY DIFFRACTION98
3.4354-3.93230.1741860.15633440X-RAY DIFFRACTION98
3.9323-4.95320.14991930.12953532X-RAY DIFFRACTION99
4.9532-44.30990.18731890.1663733X-RAY DIFFRACTION99

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