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- PDB-5tma: Zymomonas mobilis pyruvate decarboxylase mutant PDC-2.3 -

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Basic information

Entry
Database: PDB / ID: 5tma
TitleZymomonas mobilis pyruvate decarboxylase mutant PDC-2.3
ComponentsPyruvate decarboxylase
KeywordsCELL ADHESION / pyruvate decarboxylase / PDC / mutant / engineered / thermostable
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 / 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
THIAMINE DIPHOSPHATE / Pyruvate decarboxylase
Similarity search - Component
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsAlahuhta, P.M. / Lunin, V.V.
CitationJournal: Biotechnol Biofuels / Year: 2018
Title: An iterative computational design approach to increase the thermal endurance of a mesophilic enzyme.
Authors: Sammond, D.W. / Kastelowitz, N. / Donohoe, B.S. / Alahuhta, M. / Lunin, V.V. / Chung, D. / Sarai, N.S. / Yin, H. / Mittal, A. / Himmel, M.E. / Guss, A.M. / Bomble, Y.J.
History
DepositionOct 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_special_symmetry
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2Oct 4, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,43140
Polymers124,8772
Non-polymers3,55338
Water18,0871004
1
A: Pyruvate decarboxylase
B: Pyruvate decarboxylase
hetero molecules

A: Pyruvate decarboxylase
B: Pyruvate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,86180
Polymers249,7554
Non-polymers7,10776
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area22170 Å2
ΔGint-97 kcal/mol
Surface area67620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.440, 124.440, 173.825
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-935-

HOH

21A-1038-

HOH

31A-1126-

HOH

41B-969-

HOH

51B-1124-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Pyruvate decarboxylase / PDC


Mass: 62438.637 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis (bacteria) / Gene: pdc, ZMO1360 / Production host: Escherichia coli (E. coli) / References: UniProt: P06672, pyruvate decarboxylase

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Non-polymers , 5 types, 1042 molecules

#2: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1004 / 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: 2.69 Å3/Da / Density % sol: 54.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M MES monohydrate pH 6.0, 2.4 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54188 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Aug 31, 2016 / Details: HELIOS MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54188 Å / Relative weight: 1
ReflectionResolution: 1.67→101.18 Å / Num. obs: 157603 / % possible obs: 99.8 % / Redundancy: 10.41 % / Rsym value: 0.0721 / Net I/σ(I): 16.57
Reflection shellResolution: 1.67→1.7 Å / Redundancy: 4.98 % / Rmerge(I) obs: 0.7867 / Mean I/σ(I) obs: 16.57 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
PROTEUM PLUSdata reduction
Cootmodel building
PROTEUM PLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2wvg

2wvg


Resolution: 1.67→101.18 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.589 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20269 7707 4.9 %RANDOM
Rwork0.17038 ---
obs0.17201 149303 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.692 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.67→101.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8567 0 206 1004 9777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0199420
X-RAY DIFFRACTIONr_bond_other_d0.0020.028869
X-RAY DIFFRACTIONr_angle_refined_deg1.9421.95912843
X-RAY DIFFRACTIONr_angle_other_deg1.086320459
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3751220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.56625.149404
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.095151515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0691537
X-RAY DIFFRACTIONr_chiral_restr0.1270.21413
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02110887
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022050
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_it2.2332.2044757
X-RAY DIFFRACTIONr_mcbond_other2.2322.2044756
X-RAY DIFFRACTIONr_mcangle_it2.9683.2926018
X-RAY DIFFRACTIONr_mcangle_other2.9683.2936019
X-RAY DIFFRACTIONr_scbond_it3.2142.5664663
X-RAY DIFFRACTIONr_scbond_other3.2142.5664663
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7293.6996826
X-RAY DIFFRACTIONr_long_range_B_refined6.05528.22111132
X-RAY DIFFRACTIONr_long_range_B_other5.93227.61610841
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.669→1.712 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 523 -
Rwork0.363 10311 -
obs--93.94 %

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