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- PDB-8hp2: CtPDC -

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Basic information

Entry
Database: PDB / ID: 8hp2
TitleCtPDC
ComponentsPyruvate decarboxylase
KeywordsLYASE / carboxylation / fold / unit
Function / homology
Function and homology information


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-binding fold / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
Pyruvate decarboxylase
Similarity search - Component
Biological speciesCandida tropicalis (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsXu, H.H. / Song, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2023
Title: Improving tyrosol production efficiency through shortening the allosteric signal transmission distance of pyruvate decarboxylase.
Authors: Xu, H. / Yu, B. / Wei, W. / Chen, X. / Gao, C. / Liu, J. / Guo, L. / Song, W. / Liu, L. / Wu, J.
History
DepositionDec 11, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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


Theoretical massNumber of molelcules
Total (without water)124,5092
Polymers124,5092
Non-polymers00
Water00
1
A: Pyruvate decarboxylase

B: Pyruvate decarboxylase


Theoretical massNumber of molelcules
Total (without water)124,5092
Polymers124,5092
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_445x-1/2,y-1/2,z1
Buried area2530 Å2
ΔGint-14 kcal/mol
Surface area37220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.471, 85.295, 113.534
Angle α, β, γ (deg.)90.00, 120.71, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Pyruvate decarboxylase


Mass: 62254.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida tropicalis (yeast) / Gene: CTRG_03826 / Production host: Escherichia coli (E. coli) / References: UniProt: C5MDS4
Has protein modificationN

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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: 2.06 Å3/Da / Density % sol: 40.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium malonate pH 5.5, 18% Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54178 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Jan 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 3.05→47.2 Å / Num. obs: 17253 / % possible obs: 89.3 % / Redundancy: 4 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 8.9
Reflection shellResolution: 3.05→3.26 Å / Rmerge(I) obs: 0.558 / Num. unique obs: 3217

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Processing

Software
NameClassification
Aimlessdata scaling
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VJY

2vjy


Resolution: 3.05→47.2 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.876 / SU B: 62.539 / SU ML: 0.487 / Cross valid method: THROUGHOUT / ESU R Free: 0.616 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28476 813 4.7 %RANDOM
Rwork0.2325 ---
obs0.23502 16438 88.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.621 Å2
Baniso -1Baniso -2Baniso -3
1--1.91 Å20 Å20.81 Å2
2--1.34 Å2-0 Å2
3----0.23 Å2
Refinement stepCycle: 1 / Resolution: 3.05→47.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7392 0 0 0 7392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0137540
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177220
X-RAY DIFFRACTIONr_angle_refined_deg1.2261.63710241
X-RAY DIFFRACTIONr_angle_other_deg1.0591.57616642
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.025943
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.72923.788359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.614151256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0261532
X-RAY DIFFRACTIONr_chiral_restr0.040.2996
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028516
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021656
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_it0.8632.853811
X-RAY DIFFRACTIONr_mcbond_other0.8622.8493810
X-RAY DIFFRACTIONr_mcangle_it1.6284.264741
X-RAY DIFFRACTIONr_mcangle_other1.6284.2614742
X-RAY DIFFRACTIONr_scbond_it0.3562.833729
X-RAY DIFFRACTIONr_scbond_other0.3562.8313730
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.7984.2475501
X-RAY DIFFRACTIONr_long_range_B_refined3.4233.2648244
X-RAY DIFFRACTIONr_long_range_B_other3.4233.2698245
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 14811 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.05→3.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 75 -
Rwork0.308 1251 -
obs--91.76 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0922-1.309-0.51741.50720.31632.46660.0163-0.02120.10450.1844-0.03450.11630.2478-0.28430.01820.3671-0.0309-0.02350.4725-0.10390.231-17.170212.904630.8175
21.6702-0.7005-0.40390.34280.07280.61550.0168-0.1005-0.00960.0523-0.07010.00080.013-0.04590.05330.5008-0.0349-0.00680.6093-0.04690.13682.44567.31445.3384
33.353-0.08091.05350.04610.15271.1621-0.01140.03270.06350.0774-0.0461-0.0030.31040.04830.05750.48190.03520.0070.48740.05970.08972.819-0.152318.2431
42.53350.3875-0.05124.0456-2.66681.8319-0.1515-0.3025-0.04290.33330.018-0.3412-0.18130.03280.13360.3968-0.0365-0.03050.5668-0.02990.216733.852224.6827.4428
51.38060.0466-0.13710.3969-0.080.0854-0.05010.3796-0.09690.2170.01290.1028-0.1617-0.04060.03730.42540.0547-0.02070.73810.0830.086910.689635.312718.8804
63.73920.6148-0.04840.3307-0.54831.393-0.16840.73640.3180.09760.15760.025-0.1149-0.27450.01080.4186-0.036-0.02650.6960.1040.056332.82837.95414.5764
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 138
2X-RAY DIFFRACTION2A139 - 342
3X-RAY DIFFRACTION3A343 - 546
4X-RAY DIFFRACTION4B2 - 146
5X-RAY DIFFRACTION5B147 - 391
6X-RAY DIFFRACTION6B392 - 546

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