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- PDB-1rp7: E. COLI PYRUVATE DEHYDROGENASE INHIBITOR COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1rp7
TitleE. COLI PYRUVATE DEHYDROGENASE INHIBITOR COMPLEX
ComponentsPyruvate dehydrogenase E1 component
KeywordsOXIDOREDUCTASE / THDP / THIAMIN-THIAZOLONE DIPHOSPHATE / PYRUVATE DEHYDROGENASE
Function / homology
Function and homology information


: / 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 ...: / 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 / metal ion binding / identical protein binding / membrane / 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-like TK C-terminal domain / Transketolase, N-terminal / Transketolase, thiamine diphosphate binding domain / Rossmann fold - #920 ...Pyruvate dehydrogenase E1 component, N-terminal / Pyruvate dehydrogenase E1 component, middle domain / : / Pyruvate dehydrogenase E1 component middle domain / Pyruvate dehydrogenase E1 component / : / Transketolase-like TK C-terminal domain / Transketolase, N-terminal / Transketolase, thiamine diphosphate binding domain / 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
Chem-TZD / Pyruvate dehydrogenase E1 component / Pyruvate dehydrogenase E1 component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 2.09 Å
AuthorsArjunan, P. / Chandrasekhar, K. / Furey, W.
CitationJournal: Biochemistry / Year: 2004
Title: Structural Determinants of Enzyme Binding Affinity: The E1 Component of Pyruvate Dehydrogenase from Escherichia coli in Complex with the Inhibitor Thiamin Thiazolone Diphosphate.
Authors: Arjunan, P. / Chandrasekhar, K. / Sax, M. / Brunskill, A. / Nemeria, N. / Jordan, F. / Furey, W.
History
DepositionDec 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.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: Pyruvate dehydrogenase E1 component
B: Pyruvate dehydrogenase E1 component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,2446
Polymers199,3142
Non-polymers9294
Water8,989499
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13400 Å2
ΔGint-59 kcal/mol
Surface area48560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.550, 141.840, 82.170
Angle α, β, γ (deg.)90.00, 102.61, 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, Escherichia coli O157:H7
Genus: Escherichia, Escherichia / Species: , Escherichia coli / Strain: , O157:H7 / Gene: ACEE, B0114, Z0124, ECS0118 / Plasmid: JRG PGS878 / Production host: Escherichia coli (E. coli) / Strain (production host): JRG 3456
References: UniProt: P06958, UniProt: P0AFG8*PLUS, 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-TZD / 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE / THIAMIN THIAZOLONE DIPHOSPHATE


Mass: 440.306 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H18N4O8P2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / 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: 2.33 Å3/Da / Density % sol: 47.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.05
Details: PEG2000 MONOMETHYL ETHER, PROPANOL,SODIUM AZIDE, HEPES BUFFER, MAGNESIUM CHLORIDE, THIAMIN-THIAZOLONE DIPHOSPHATE, pH 7.05, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Crystal-IDSol-IDDetails
115-20 %1reservoir
25-10 %1reservoir
30.2 %1reservoir
4100 mM1reservoirpH7.05

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.072 / Wavelength: 1.072 Å
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: 2.09→40.6 Å / Num. all: 107597 / Num. obs: 100232 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 16.65
Reflection shellResolution: 2.09→2.15 Å / Redundancy: 1.23 % / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 3.84 / Num. unique all: 8714 / Rsym value: 0.203 / % possible all: 55.1
Reflection
*PLUS
Highest resolution: 2.09 Å / Num. measured all: 351214
Reflection shell
*PLUS
% possible obs: 55.1 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: 1L8A

1l8a


Resolution: 2.09→8 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 5521 6 %RANDOM
Rwork0.192 ---
all0.205 95734 --
obs0.192 90869 84.5 %-
Displacement parametersBiso mean: 18.16 Å2
Refine analyzeLuzzati coordinate error obs: 0.08 Å
Refinement stepCycle: LAST / Resolution: 2.09→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12682 0 56 499 13237
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.27
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.97
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.68
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.8591.5
X-RAY DIFFRACTIONx_mcangle_it2.6762
X-RAY DIFFRACTIONx_scbond_it3.2042
X-RAY DIFFRACTIONx_scangle_it4.542.5
LS refinement shellResolution: 2.09→2.2 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.273 474 6 %
Rwork0.238 6832 -
obs-7306 47.9 %
Refinement
*PLUS
Num. reflection obs: 85348
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.267
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.97
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.68

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