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- PDB-2q5l: X-ray structure of phenylpyruvate decarboxylase in complex with 2... -

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Basic information

Entry
Database: PDB / ID: 2q5l
TitleX-ray structure of phenylpyruvate decarboxylase in complex with 2-(1-hydroxyethyl)-3-deaza-ThDP
ComponentsPHENYLPYRUVATE DECARBOXYLASE
KeywordsLYASE / thiamine diphosphate / asymmetric dimer of dimers / open active site loop / covalent intermediate analogue
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
Chem-R1T / Chem-S1T / Indole-3-pyruvate decarboxylase
Similarity search - Component
Biological speciesAzospirillum brasilense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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)122,82712
Polymers120,6542
Non-polymers2,17310
Water18,1951010
1
A: PHENYLPYRUVATE DECARBOXYLASE
B: PHENYLPYRUVATE DECARBOXYLASE
hetero molecules

A: PHENYLPYRUVATE DECARBOXYLASE
B: PHENYLPYRUVATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,65424
Polymers241,3074
Non-polymers4,34620
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10450 Å2
ΔGint-130 kcal/mol
Surface area35220 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)99.978, 179.050, 120.858
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
11B-4397-

HOH

21B-4464-

HOH

DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operation: -x,y,-1/2-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, 1020 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-S1T / 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-[(1S)-1-HYDROXYETHYL]-3-METHYL-2-THIENYL}ETHYL TRIHYDROGEN DIPHOSPHATE / 2-[(1S)-1-HYDROXYETHYL]-3-DEAZA-THDP


Mass: 467.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N3O8P2S
#5: Chemical ChemComp-R1T / 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-[(1R)-1-HYDROXYETHYL]-3-METHYL-2-THIENYL}ETHYL TRIHYDROGEN DIPHOSPHATE / 2-[(1R)-1-HYDROXYETHYL]-3-DEAZA-THDP


Mass: 467.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N3O8P2S
#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.: 1010 / 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: 2.24 Å3/Da / Density % sol: 45.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15% PEG4000, 10% glycerol, 100 mM Hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8157 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 1, 2005
RadiationMonochromator: Si[111], horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8157 Å / Relative weight: 1
ReflectionResolution: 1.85→32.5 Å / Num. all: 92575 / Num. obs: 90993 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 19.24 Å2 / Rsym value: 0.084 / Net I/σ(I): 24.1
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 9173 / Rsym value: 0.44 / % possible all: 96

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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: 1.85→32.5 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.204 4544 -RANDOM
Rwork0.17 ---
obs0.17 90993 98.4 %-
all-92441 --
Refinement stepCycle: LAST / Resolution: 1.85→32.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7933 0 132 1010 9075
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.458
X-RAY DIFFRACTIONc_bond_d0.0089
LS refinement shellResolution: 1.85→1.86 Å
RfactorNum. reflection
Rfree0.2241 79
Rwork0.2362 -
obs-1750

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