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- PDB-2g28: E. Coli Pyruvate Dehydrogenase H407A variant Phosphonolactylthiam... -

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Basic information

Entry
Database: PDB / ID: 2g28
TitleE. Coli Pyruvate Dehydrogenase H407A variant Phosphonolactylthiamin Diphosphate Complex
ComponentsPyruvate dehydrogenase E1 component
KeywordsOXIDOREDUCTASE / PLTHDP / PHOSPHONOLACTYLTHIAMIN DIPHOSPHATE / PYRUVATE DEHYDROGENASE E1 COMPONENT
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 / molecular adaptor activity / magnesium ion binding / protein homodimerization 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 / molecular adaptor activity / magnesium ion binding / protein homodimerization activity / 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 / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II ...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-TDK / 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: 2006
Title: A Thiamin-bound, Pre-decarboxylation Reaction Intermediate Analogue in the Pyruvate Dehydrogenase E1 Subunit Induces Large Scale Disorder-to-Order Transformations in the Enzyme and Reveals ...Title: A Thiamin-bound, Pre-decarboxylation Reaction Intermediate Analogue in the Pyruvate Dehydrogenase E1 Subunit Induces Large Scale Disorder-to-Order Transformations in the Enzyme and Reveals Novel Structural Features in the Covalently Bound Adduct.
Authors: Arjunan, P. / Sax, M. / Brunskill, A. / Chandrasekhar, K. / Nemeria, N. / Zhang, S. / Jordan, F. / Furey, W.
History
DepositionFeb 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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_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

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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)200,4906
Polymers199,3142
Non-polymers1,1754
Water9,890549
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13900 Å2
ΔGint-74 kcal/mol
Surface area49820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.990, 143.200, 82.530
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 (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-TDK / 3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-{(1S)-1-HYDROXY-1-[(R)-HYDROXY(METHOXY)PHOSPHORYL]ETHYL}-5-(2-{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM / 2-PHOSPHONOLACTYLTHIAMIN DIPHOSPHATE


Mass: 563.373 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H26N4O11P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 549 / 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: 2.37 Å3/Da / Density % sol: 48.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.05
Details: PEG2000 MONOMETHYL ETHER, PROPANOL, SODIUM AZIDE, HEPES BUFFER, MAGNESIUM CHLORIDE, PHOSPHONOLACTYL- THIAMIN DIPHOSPHATE, PH 7.00, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K, pH 7.05

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.00013 / Wavelength: 1.00013 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 12, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00013 Å / Relative weight: 1
ReflectionResolution: 1.55→41.77 Å / Num. all: 237104 / Num. obs: 213020 / % possible obs: 79.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 12.26
Reflection shellResolution: 1.55→1.67 Å / Mean I/σ(I) obs: 1.46 / % possible all: 32.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
PHASESphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: 1L8A

1l8a


Resolution: 1.85→41.77 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 558340.6 / 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
Rfree0.24 7535 5 %RANDOM
Rwork0.216 ---
all0.227 157076 --
obs0.216 150327 95.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.6727 Å2 / ksol: 0.373614 e/Å3
Displacement parametersBiso mean: 21.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.81 Å20 Å20.48 Å2
2--0.79 Å20 Å2
3---1.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.85→41.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12682 0 70 549 13301
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_mcbond_it0.2551.5
X-RAY DIFFRACTIONc_mcangle_it0.4692
X-RAY DIFFRACTIONc_scbond_it0.2462
X-RAY DIFFRACTIONc_scangle_it0.4112.5
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3 1137 4.9 %
Rwork0.267 21906 -
obs--87.7 %

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