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- PDB-2iea: E. coli pyruvate dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 2iea
TitleE. coli pyruvate dehydrogenase
ComponentsPyruvate dehydrogenase E1 component
KeywordsOXIDOREDUCTASE / THIAMIN DIPHOSPHATE / PYRUVATE / ALPHA-KETO ACID DEHYDROGENASE
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 / MAD / Resolution: 1.85 Å
AuthorsFurey, W. / Arjunan, P.
CitationJournal: Biochemistry / Year: 2002
Title: Structure of the pyruvate dehydrogenase multienzyme complex E1 component from Escherichia coli at 1.85 A resolution.
Authors: Arjunan, P. / Nemeria, N. / Brunskill, A. / Chandrasekhar, K. / Sax, M. / Yan, Y. / Jordan, F. / Guest, J.R. / Furey, W.
History
DepositionSep 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Aug 4, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / 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_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.ptnr1_label_seq_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.ptnr3_label_seq_id / _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.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_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 2.1Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water12,286682
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13380 Å2
ΔGint-59 kcal/mol
Surface area49300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.690, 141.600, 82.460
Angle α, β, γ (deg.)90.00, 102.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Pyruvate dehydrogenase E1 component


Mass: 99657.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: aceE / Plasmid: JRG 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.: 682 / 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: 2.34 Å3/Da / Density % sol: 47.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.05
Details: PEG2000 MONOMETHYL ETHER, PROPANOL, SODIUM AZIDE, HEPES BUFFER, MAGNESIUM CHLORIDE, THIAMIN DIPHOSPHATE, pH 7.05, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.072
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Jan 27, 2000 / Details: TOROIDAL MIRROR
RadiationMonochromator: CURVED SILICON MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. all: 149133 / Num. obs: 146183 / % possible obs: 92.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Biso Wilson estimate: 11.5 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 17.9
Reflection shellResolution: 1.85→1.94 Å / Redundancy: 2.23 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 3.9 / Num. unique all: 8471 / Rsym value: 0.175 / % possible all: 70.2

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Processing

Software
NameVersionClassification
PHASESphasing
CNS1.1refinement
MAR345345DTBdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.85→8 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 208869.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1
Details: THIS DEPOSITION UPDATES THE COORDINATES OF 1L8A AFTER VALIDATION THROUGH MOLPROBITY (I. W. DAVIS ET AL., NUCL. ACIDS RES. 32, W615-W619, 2004) AND MINIMIZATION WITH CNS (BRUNGER ET AL. ACTA ...Details: THIS DEPOSITION UPDATES THE COORDINATES OF 1L8A AFTER VALIDATION THROUGH MOLPROBITY (I. W. DAVIS ET AL., NUCL. ACIDS RES. 32, W615-W619, 2004) AND MINIMIZATION WITH CNS (BRUNGER ET AL. ACTA CRYST. D54, 905-921, 1998). THE MAIN DIFFERENCE BETWEEN THIS DEPOSITION AND THE ORIGINAL ONE IS THE INTERCHANGE OF NITROGEN AND OXYGEN ATOMS IN SOME AMIDE SIDE CHAINS, AND INTERCHANGE OF NITROGEN AND CARBON ATOMS IN SOME HISTIDINE SIDE CHAINS. THIS DEPOSITION IS BETTER SUITED FOR DETAILED COMPARISONS WITH THE APO AND INHIBITED STRUCTURES 2G67, 1RP7, 2G25 AND 2G28 AS THOSE SUBSEQUENTLY DETERMINED STRUCTURES WERE ALSO TREATED IN THE SAME MANNER. KEY STRUCTURAL DETAILS AND INTERACTIONS DESCRIBED IN OUR 2002 PAPER IN 'BIOCHEMISTRY' HOWEVER, REMAIN UNCHANGED.
RfactorNum. reflection% reflectionSelection details
Rfree0.203 8130 6.1 %RANDOM
Rwork0.177 ---
all0.19 149133 --
obs0.177 133768 87 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 68.3358 Å2 / ksol: 0.508805 e/Å3
Displacement parametersBiso mean: 19.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å21.76 Å2
2---0.6 Å20 Å2
3---0.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.85→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12682 0 54 682 13418
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it2.2221.5
X-RAY DIFFRACTIONc_mcangle_it2.7512
X-RAY DIFFRACTIONc_scbond_it3.6442
X-RAY DIFFRACTIONc_scangle_it4.8122.5
LS refinement shellResolution: 1.85→1.92 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.232 540 6 %
Rwork0.2 8471 -
obs--58.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramtoph19x_new.tdp
X-RAY DIFFRACTION3param19x_new.tdp

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