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- PDB-6efg: Pyruvate decarboxylase from Kluyveromyces lactis -

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Basic information

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


pyruvate decarboxylase / pyruvate decarboxylase activity / thiamine pyrophosphate binding / magnesium ion binding
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
THIAMINE DIPHOSPHATE / Pyruvate decarboxylase
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 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: FEBS J. / Year: 2006
Title: The crystal structure of pyruvate decarboxylase from Kluyveromyces lactis. Implications for the substrate activation mechanism of this enzyme.
Authors: Kutter, S. / Wille, G. / Relle, S. / Weiss, M.S. / Hubner, G. / 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.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

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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
D: Pyruvate decarboxylase
E: Pyruvate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,66612
Polymers246,8674
Non-polymers1,7988
Water5,549308
1
A: Pyruvate decarboxylase
B: Pyruvate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,3336
Polymers123,4342
Non-polymers8994
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7500 Å2
ΔGint-61 kcal/mol
Surface area37660 Å2
MethodPISA
2
D: Pyruvate decarboxylase
E: Pyruvate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,3336
Polymers123,4342
Non-polymers8994
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7600 Å2
ΔGint-64 kcal/mol
Surface area37560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.360, 78.480, 100.570
Angle α, β, γ (deg.)80.10, 67.72, 77.40
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Pyruvate decarboxylase /


Mass: 61716.762 Da / Num. of mol.: 4 / 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
#2: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


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


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 308 / 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 %
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 30 seconds in 2 uL mother liquor + 2 uL 15% w/v glycerol, 200 mM acetaldehyde prior to flash freezing.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.00001 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 21, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.04→38.25 Å / Num. obs: 126964 / % possible obs: 93.2 % / Redundancy: 2.7 % / Biso Wilson estimate: 24.75 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.065 / Rrim(I) all: 0.109 / Net I/σ(I): 8.6
Reflection shellResolution: 2.04→2.08 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4511 / CC1/2: 0.689 / Rpim(I) all: 0.508 / Rrim(I) all: 0.837 / % possible all: 66.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
xia20.5.492-g24d9851b-dials-1.8data reduction
XDS20180409data reduction
Aimless0.6.3data scaling
MOLREP11.6.04phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2VK4

2vk4


Resolution: 2.04→38.25 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.891 / SU B: 9.157 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.223 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2903 970 0.8 %RANDOM
Rwork0.22069 ---
obs0.22123 125994 93.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.997 Å2
Baniso -1Baniso -2Baniso -3
1--1.7 Å2-1.22 Å2-0.76 Å2
2---1.37 Å20.62 Å2
3---1.55 Å2
Refinement stepCycle: 1 / Resolution: 2.04→38.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16531 0 108 308 16947
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01416986
X-RAY DIFFRACTIONr_bond_other_d0.0010.01715486
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.66123137
X-RAY DIFFRACTIONr_angle_other_deg0.9191.63536202
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.72652133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.90323.607793
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.669152797
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9431572
X-RAY DIFFRACTIONr_chiral_restr0.0690.22293
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218966
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023046
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_it2.983.7648562
X-RAY DIFFRACTIONr_mcbond_other2.983.7638561
X-RAY DIFFRACTIONr_mcangle_it4.4025.63110682
X-RAY DIFFRACTIONr_mcangle_other4.4015.63210683
X-RAY DIFFRACTIONr_scbond_it3.0954.0448424
X-RAY DIFFRACTIONr_scbond_other3.0954.0448425
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7195.94512455
X-RAY DIFFRACTIONr_long_range_B_refined7.01445.03719349
X-RAY DIFFRACTIONr_long_range_B_other7.01445.03419332
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.044→2.097 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 56 -
Rwork0.38 7349 -
obs--73.66 %

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