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- PDB-2q5q: X-ray structure of phenylpyruvate decarboxylase in complex with 3... -

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Basic information

Entry
Database: PDB / ID: 2q5q
TitleX-ray structure of phenylpyruvate decarboxylase in complex with 3-deaza-ThDP and 5-phenyl-2-oxo-valeric acid
ComponentsPhenylpyruvate decarboxylase
KeywordsLYASE / thiamine diphosphate / symmetrical dimer of dimers / closed active site loops / substrate complex
Function / homology
Function and homology information


indolepyruvate decarboxylase / indolepyruvate decarboxylase activity / auxin biosynthetic process / aromatic amino acid family catabolic process to alcohol via Ehrlich pathway / pyruvate decarboxylase activity / thiamine pyrophosphate binding / magnesium ion binding / cytosol
Similarity search - Function
Indole-3-pyruvate decarboxylase / Thiamine pyrophosphate (TPP)-dependent enzyme / : / 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 ...Indole-3-pyruvate decarboxylase / Thiamine pyrophosphate (TPP)-dependent enzyme / : / 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
5-PHENYL-2-KETO-VALERIC ACID / L(+)-TARTARIC ACID / Chem-TPW / Indole-3-pyruvate decarboxylase
Similarity search - Component
Biological speciesAzospirillum brasilense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsVersees, W. / Spaepen, S. / Wood, M.D. / Leeper, F.J. / Vanderleyden, J. / Steyaert, J.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Molecular mechanism of allosteric substrate activation in a thiamine diphosphate-dependent decarboxylase.
Authors: Versees, W. / Spaepen, S. / Wood, M.D. / Leeper, F.J. / Vanderleyden, J. / Steyaert, J.
History
DepositionJun 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Aug 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 / diffrn_source / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE Authors state there is an error in the database sequence. The correct residue at position 327 is ARG.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)122,65213
Polymers120,6542
Non-polymers1,99811
Water20,1231117
1
A: Phenylpyruvate decarboxylase
B: Phenylpyruvate decarboxylase
hetero molecules

A: Phenylpyruvate decarboxylase
B: Phenylpyruvate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,30426
Polymers241,3074
Non-polymers3,99722
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11600 Å2
ΔGint-32 kcal/mol
Surface area33610 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)74.688, 145.120, 194.107
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-5326-

HOH

21B-5496-

HOH

31B-5514-

HOH

DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operation: x,-y+1,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Phenylpyruvate decarboxylase / PPDC


Mass: 60326.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azospirillum brasilense (bacteria) / Gene: ipdC / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus-RP / References: UniProt: P51852, phenylpyruvate decarboxylase

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Non-polymers , 6 types, 1128 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-TPW / 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE / 3-DEAZA-THDP


Mass: 423.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H19N3O7P2S
#4: Chemical
ChemComp-KPV / 5-PHENYL-2-KETO-VALERIC ACID / 2-OXO-5-PHENYLPENTANOIC ACID


Mass: 192.211 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H12O3
#5: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1117 / 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: 2.18 Å3/Da / Density % sol: 43.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 11% PEG3350, 0.2 M di-ammonium tartrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9732 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 30, 2006
RadiationMonochromator: Fixed exit double crystal Si [111], horizontally focussing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9732 Å / Relative weight: 1
ReflectionResolution: 1.9→34.9 Å / Num. all: 83208 / Num. obs: 76991 / % possible obs: 92.5 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 20.54 Å2 / Rsym value: 0.074 / Net I/σ(I): 18.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.45 / Num. unique all: 8220 / Rsym value: 0.48 / % possible all: 92

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Processing

Software
NameVersionClassification
DENZOdata reduction
PHASERphasing
CNS1.1refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2NXW

2nxw


Resolution: 1.9→34.9 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.206 3831 -RANDOM
Rwork0.163 ---
obs0.163 76991 92.5 %-
all-83208 --
Refinement stepCycle: LAST / Resolution: 1.9→34.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7936 0 132 1117 9185
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.43
X-RAY DIFFRACTIONc_bond_d0.009
LS refinement shellResolution: 1.9→1.91 Å
RfactorNum. reflection
Rfree0.356 57
Rwork0.292 -
obs-1450

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