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- PDB-2nxw: Crystal structure of phenylpyruvate decarboxylase of Azospirillum... -

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Basic information

Entry
Database: PDB / ID: 2nxw
TitleCrystal structure of phenylpyruvate decarboxylase of Azospirillum brasilense
ComponentsPHENYL-3-PYRUVATE DECARBOXYLASE
KeywordsLYASE / thiamine pyrophosphate / asymmetric dimer of dimers / open active site loops
Function / homology
Function and homology information


auxin biosynthetic process / indolepyruvate decarboxylase / indolepyruvate decarboxylase activity / 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
THIAMINE DIPHOSPHATE / Indole-3-pyruvate decarboxylase
Similarity search - Component
Biological speciesAzospirillum brasilense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsVersees, W. / Spaepen, S. / Vanderleyden, J. / Steyaert, J.
CitationJournal: Febs J. / Year: 2007
Title: The crystal structure of phenylpyruvate decarboxylase from Azospirillum brasilense at 1.5 A resolution. Implications for its catalytic and regulatory mechanism.
Authors: Versees, W. / Spaepen, S. / Vanderleyden, J. / Steyaert, J.
History
DepositionNov 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHENYL-3-PYRUVATE DECARBOXYLASE
B: PHENYL-3-PYRUVATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,90011
Polymers120,6542
Non-polymers1,2469
Water24,0861337
1
A: PHENYL-3-PYRUVATE DECARBOXYLASE
B: PHENYL-3-PYRUVATE DECARBOXYLASE
hetero molecules

A: PHENYL-3-PYRUVATE DECARBOXYLASE
B: PHENYL-3-PYRUVATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,80022
Polymers241,3074
Non-polymers2,49318
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8730 Å2
ΔGint-107 kcal/mol
Surface area35600 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)99.411, 179.032, 120.925
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-4359-

HOH

21A-4668-

HOH

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

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PHENYL-3-PYRUVATE DECARBOXYLASE / PHENYL-3-PYRUVATE DECARBOXYLASE


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 , 5 types, 1346 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-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1337 / 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: 2.23 Å3/Da / Density % sol: 44.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG 4000, 10 % glycerol, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8131 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 14, 2005
RadiationMonochromator: Si [111], horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8131 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 171465 / Num. obs: 170507 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 21.37
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 3.54 / Num. unique all: 16945 / % possible all: 99.1

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Processing

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

1ovm


Resolution: 1.5→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.196 8539 -RANDOM
Rwork0.175 ---
all0.175 171465 --
obs0.175 170507 99.4 %-
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7863 0 74 1337 9274
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.405581
X-RAY DIFFRACTIONc_bond_d0.008115
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.006
RfactorNum. reflection% reflection
Rfree0.23 1408 -
Rwork0.218 --
obs-26724 99.2 %

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