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- PDB-6efh: Pyruvate decarboxylase from Kluyveromyces lactis soaked with pyru... -

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Basic information

Entry
Database: PDB / ID: 6efh
TitlePyruvate decarboxylase from Kluyveromyces lactis soaked with pyruvamide
ComponentsPyruvate decarboxylase
KeywordsLYASE / pyruvate decarboxylase / thiamine diphosphate / substrate activation / pyruvamide
Function / homology
Function and homology information


pyruvate decarboxylase / aromatic amino acid family catabolic process to alcohol via Ehrlich pathway / pyruvate decarboxylase activity / thiamine pyrophosphate binding / magnesium ion binding / nucleus / cytosol
Similarity search - Function
: / : / Thiamine pyrophosphate (TPP)-dependent enzyme / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding ...: / : / Thiamine pyrophosphate (TPP)-dependent enzyme / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain / Thiamin diphosphate-binding fold / DHS-like NAD/FAD-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(1S,2S)-1-amino-1,2-dihydroxypropan-1-olate / THIAMINE DIPHOSPHATE / Pyruvate decarboxylase
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsKutter, S. / Konig, S.
Citation
Journal: To be Published
Title: The crystal structures of pyruvate decarboxylase from Kluyveromyces lactis in the absence of ligands and in the presence of the substrate surrogate pyruvamide
Authors: Kutter, S. / Konig, S.
#1: Journal: J. Biol. Chem. / Year: 2009
Title: Covalently bound substrate at the regulatory site of yeast pyruvate decarboxylases triggers allosteric enzyme activation.
Authors: Kutter, S. / Weiss, M.S. / Wille, G. / Golbik, R. / Spinka, M. / Konig, S.
History
DepositionAug 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyruvate decarboxylase
B: Pyruvate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,7839
Polymers123,4342
Non-polymers1,3507
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, doi: 10.1074/jbc.M806228200 10.1111/j.1742-4658.2006.05415.x doi: 10.5281/zenodo.1314666
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9160 Å2
ΔGint-69 kcal/mol
Surface area37100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.765, 172.765, 210.083
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Pyruvate decarboxylase


Mass: 61716.762 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
References: UniProt: Q12629, pyruvate decarboxylase

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Non-polymers , 5 types, 48 molecules

#2: Chemical ChemComp-PY0 / (1S,2S)-1-amino-1,2-dihydroxypropan-1-olate


Mass: 106.101 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8NO3
#3: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 3.22 Å3/Da / Density % sol: 61.8 %
Crystal growTemperature: 281.15 K / Method: vapor diffusion, hanging drop / pH: 6.25
Details: 2 mg/mL KlPDC in 2 mM MES, 18 mM citrate, pH 6.25, 4 mM thiamine diphosphate, 4 mM magnesium sulfate, 2 mM DTT, 1:1 with mother liquor (18-24% w/v PEG2000/PEG6000), ~25 days at 8 degrees C, ...Details: 2 mg/mL KlPDC in 2 mM MES, 18 mM citrate, pH 6.25, 4 mM thiamine diphosphate, 4 mM magnesium sulfate, 2 mM DTT, 1:1 with mother liquor (18-24% w/v PEG2000/PEG6000), ~25 days at 8 degrees C, soaked for 50 seconds in 2 uL mother liquor + 2 uL 90% v/v PEG400, 200 mM pyruvamide prior to flash freezing

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 7, 2007
RadiationMonochromator: Diamond (001) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.99→55.6 Å / Num. obs: 32279 / % possible obs: 100 % / Redundancy: 14.4 % / Biso Wilson estimate: 25.68 Å2 / Rmerge(I) obs: 0.333 / Net I/σ(I): 9
Reflection shellResolution: 2.99→3.05 Å / Redundancy: 14.7 % / Rmerge(I) obs: 1.797 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1591 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
xia20.5.492-g24d9851b-dials-1.8data reduction
MOSFLM7.2.2data reduction
Aimless0.6.3data scaling
MOLREP11.6.04phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2VK4

2vk4


Resolution: 2.99→55.6 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.846 / SU B: 20.033 / SU ML: 0.351 / Cross valid method: THROUGHOUT / ESU R Free: 0.423 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1055 3.3 %RANDOM
Rwork0.178 ---
obs0.181 31223 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.52 Å2
Baniso -1Baniso -2Baniso -3
1-1.94 Å20 Å20 Å2
2--1.94 Å20 Å2
3----3.89 Å2
Refinement stepCycle: LAST / Resolution: 2.99→55.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8587 0 84 41 8712
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0148853
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178037
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.66512059
X-RAY DIFFRACTIONr_angle_other_deg0.8591.64218790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.40651110
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.60923.641412
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.268151447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3271536
X-RAY DIFFRACTIONr_chiral_restr0.0640.21192
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029880
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021602
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2134.3064449
X-RAY DIFFRACTIONr_mcbond_other3.24.3054448
X-RAY DIFFRACTIONr_mcangle_it5.176.455556
X-RAY DIFFRACTIONr_mcangle_other5.1696.4515557
X-RAY DIFFRACTIONr_scbond_it2.9854.4594404
X-RAY DIFFRACTIONr_scbond_other2.9854.4594404
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8826.616504
X-RAY DIFFRACTIONr_long_range_B_refined7.52650.0999791
X-RAY DIFFRACTIONr_long_range_B_other7.52650.1029792
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.99→3.07 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 76 -
Rwork0.308 2239 -
obs--100 %

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