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

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Basic information

Entry
Database: PDB / ID: 4bnp
Title3D structure of E. coli Isocitrate Dehydrogenase K100M mutant in complex with isocitrate and magnesium(II)
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
ISOCITRIC ACID / Isocitrate dehydrogenase [NADP]
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMiller, S.P. / Goncalves, S. / Matias, P.M. / Dean, A.M.
CitationJournal: Chembiochem / Year: 2014
Title: Evolution of a Transition State: Role of Lys100 in the Active Site of Isocitrate Dehydrogenase.
Authors: Miller, S.P. / Goncalves, S. / Matias, P.M. / Dean, A.M.
History
DepositionMay 16, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2014Group: Database references
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Dec 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 / 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 / _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)46,1244
Polymers45,8121
Non-polymers3123
Water9,476526
1
A: ISOCITRATE DEHYDROGENASE [NADP]
hetero molecules

A: ISOCITRATE DEHYDROGENASE [NADP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,2488
Polymers91,6232
Non-polymers6256
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8300 Å2
ΔGint-88.7 kcal/mol
Surface area31330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.562, 102.562, 150.645
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#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) / Strain (production host): K-12
References: UniProt: P08200, isocitrate dehydrogenase (NADP+)
#2: Chemical ChemComp-ICT / ISOCITRIC ACID


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 526 / 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: 4.5 Å3/Da / Density % sol: 72 % / Description: NONE
Crystal growpH: 5.8
Details: A SOLUTION OF THE LYS100MET MUTANT (20 MG/ML PROTEIN IN 0.9 MM CITRIC ACID, 3.5 MM NA2HPO4 PH 6.0, 100 MM NACL, 0.02% NAN3 AND 2 MM DTT) WAS MIXED 1:1 WITH A CRYSTALLIZATION SOLUTION (1.85 M ...Details: A SOLUTION OF THE LYS100MET MUTANT (20 MG/ML PROTEIN IN 0.9 MM CITRIC ACID, 3.5 MM NA2HPO4 PH 6.0, 100 MM NACL, 0.02% NAN3 AND 2 MM DTT) WAS MIXED 1:1 WITH A CRYSTALLIZATION SOLUTION (1.85 M NH4SO4, 50 MM CITRIC ACID/NA2HPO4, 0.1 M NACL AND 0.2 M DTT AT PH 5.8) AND 2 UL DROPS EQUILIBRATED AGAINST 500 UL OF THE CRYSTALLIZATION SOLUTION. TETRAGONAL BIPYRAMIDAL CRYSTALS, 300 UM X 150 UM X 75 UM, DEVELOPED WITHIN 5 DAYS.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418
DetectorType: BRUKER AXS PROTEUM X8 PT135 / Detector: CCD / Date: Jun 16, 2008
RadiationMonochromator: MONTEL MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→52.2 Å / Num. obs: 55032 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 19.11 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.5
Reflection shellResolution: 2→2.1 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.2_1309)refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AI2

1ai2


Resolution: 2→51.281 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 17.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1915 2773 5.1 %
Rwork0.1631 --
obs0.1645 54942 99.98 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→51.281 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3204 0 19 526 3749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083356
X-RAY DIFFRACTIONf_angle_d1.0274548
X-RAY DIFFRACTIONf_dihedral_angle_d11.9681276
X-RAY DIFFRACTIONf_chiral_restr0.072504
X-RAY DIFFRACTIONf_plane_restr0.004594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.03450.28781490.25312564X-RAY DIFFRACTION100
2.0345-2.07150.25241360.23262572X-RAY DIFFRACTION100
2.0715-2.11130.23381300.21292563X-RAY DIFFRACTION100
2.1113-2.15440.24491360.20972565X-RAY DIFFRACTION100
2.1544-2.20130.19771330.19152575X-RAY DIFFRACTION100
2.2013-2.25250.23931590.19232565X-RAY DIFFRACTION100
2.2525-2.30880.20041540.17972552X-RAY DIFFRACTION100
2.3088-2.37120.22851320.17512564X-RAY DIFFRACTION100
2.3712-2.4410.19331420.17342593X-RAY DIFFRACTION100
2.441-2.51980.19071480.16642576X-RAY DIFFRACTION100
2.5198-2.60980.21391210.16262600X-RAY DIFFRACTION100
2.6098-2.71430.17061290.16342589X-RAY DIFFRACTION100
2.7143-2.83790.19591290.16072612X-RAY DIFFRACTION100
2.8379-2.98750.20921320.15892607X-RAY DIFFRACTION100
2.9875-3.17460.1861260.14912612X-RAY DIFFRACTION100
3.1746-3.41970.18431520.14522629X-RAY DIFFRACTION100
3.4197-3.76370.18491400.1342627X-RAY DIFFRACTION100
3.7637-4.30810.14011470.11992655X-RAY DIFFRACTION100
4.3081-5.42680.15541430.13382689X-RAY DIFFRACTION100
5.4268-51.29780.17661350.18422860X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.74470.048-0.30231.5367-0.07151.81220.0851-0.04980.29980.05530.01980.0088-0.3905-0.044-0.07790.16720.03250.03830.128-0.02810.1655-42.8455-2.081712.831
20.7159-0.25-0.08110.74090.14361.1765-0.0399-0.14460.04790.04220.0434-0.0998-0.06320.17540.01340.0905-0.0029-0.00790.1281-0.0270.116-20.4155-20.163910.3338
31.828-0.3622-0.25570.74820.21530.9666-0.01980.08-0.06550.0086-0.00540.10050.0395-0.15410.01970.0946-0.01610.02550.120.00020.0999-43.2547-20.31658.8076
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 2:113)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 114:291)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 292:416)

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