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- PDB-2qta: E. coli Pyruvate dehydrogenase E1 component E401K mutant with thi... -

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Basic information

Entry
Database: PDB / ID: 2qta
TitleE. coli Pyruvate dehydrogenase E1 component E401K mutant with thiamin diphosphate
ComponentsPyruvate dehydrogenase E1 component
KeywordsOXIDOREDUCTASE / pyruvate dehydrogenase / thiamin diphosphate / Glycolysis / Magnesium / Metal-binding / Thiamine pyrophosphate
Function / homology
Function and homology information


: / pyruvate dehydrogenase activity / pyruvate dehydrogenase (acetyl-transferring) / pyruvate dehydrogenase (acetyl-transferring) activity / pyruvate catabolic process / pyruvate dehydrogenase complex / thiamine pyrophosphate binding / small molecule binding / glycolytic process / molecular adaptor activity ...: / pyruvate dehydrogenase activity / pyruvate dehydrogenase (acetyl-transferring) / pyruvate dehydrogenase (acetyl-transferring) activity / pyruvate catabolic process / pyruvate dehydrogenase complex / thiamine pyrophosphate binding / small molecule binding / glycolytic process / molecular adaptor activity / magnesium ion binding / protein homodimerization activity / membrane / identical protein binding / cytosol
Similarity search - Function
Pyruvate dehydrogenase E1 component, N-terminal / Pyruvate dehydrogenase E1 component, middle domain / Pyruvate dehydrogenase E1 component middle domain / Pyruvate dehydrogenase E1 component / Transketolase, thiamine diphosphate binding domain / Transketolase, N-terminal / Rossmann fold - #920 / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / Thiamin diphosphate-binding fold ...Pyruvate dehydrogenase E1 component, N-terminal / Pyruvate dehydrogenase E1 component, middle domain / Pyruvate dehydrogenase E1 component middle domain / Pyruvate dehydrogenase E1 component / Transketolase, thiamine diphosphate binding domain / Transketolase, N-terminal / Rossmann fold - #920 / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / Thiamin diphosphate-binding fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THIAMINE DIPHOSPHATE / Pyruvate dehydrogenase E1 component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 1.85 Å
AuthorsFurey, W. / Arjunan, P. / Chandrasekhar, K.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: A Dynamic Loop at the Active Center of the Escherichia coli Pyruvate Dehydrogenase Complex E1 Component Modulates Substrate Utilization and Chemical Communication with the E2 Component
Authors: Kale, S. / Arjunan, P. / Furey, W. / Jordan, F.
History
DepositionAug 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 15, 2012Group: Structure summary
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 2.0Aug 4, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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_ref_seq_dif.details / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyruvate dehydrogenase E1 component
B: Pyruvate dehydrogenase E1 component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,2146
Polymers199,3142
Non-polymers8994
Water7,440413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.810, 141.830, 82.560
Angle α, β, γ (deg.)90.00, 102.01, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe two molecules in the asymmetric unit constitute the biological unit, which is a dimer containing a noncrystallographic twofold axis.

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Components

#1: Protein Pyruvate dehydrogenase E1 component


Mass: 99657.234 Da / Num. of mol.: 2 / Mutation: E401K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: aceE / Plasmid: pGS878 / Production host: Escherichia coli (E. coli) / Strain (production host): JRG 3456
References: UniProt: P0AFG8, pyruvate dehydrogenase (acetyl-transferring)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 2.35 Å3/Da / Density % sol: 47.67 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.05
Details: PEG 2000 monomethyl ether, proponal, sodium azide, hepes buffer, magnesium chloride, thiamin diphosphate, pH 7.05, Vapour diffusion, temperature 295K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 16, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→38.06 Å / Num. all: 155239 / Num. obs: 151931 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 27.92
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 6 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 7.7 / Num. unique all: 14769 / Rsym value: 0.336 / % possible all: 94.2

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT3data extraction
MAR345data collection
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 2IEA

2iea


Resolution: 1.85→38.06 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 106137.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.237 7685 5.1 %RANDOM
Rwork0.214 ---
all0.225 151931 --
obs0.225 151931 97.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.722 Å2 / ksol: 0.334 e/Å3
Displacement parametersBiso mean: 20.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å22.15 Å2
2---2.94 Å20 Å2
3---3.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.85→38.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12682 0 54 413 13149
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_mcbond_it0.2571.5
X-RAY DIFFRACTIONc_mcangle_it0.482
X-RAY DIFFRACTIONc_scbond_it0.212
X-RAY DIFFRACTIONc_scangle_it0.3652.5
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.272 1236 5.2 %
Rwork0.246 22566 -
all-23802 -
obs-23802 91.5 %

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