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- PDB-1ovm: Crystal structure of Indolepyruvate decarboxylase from Enterobact... -

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Basic information

Entry
Database: PDB / ID: 1ovm
TitleCrystal structure of Indolepyruvate decarboxylase from Enterobacter cloacae
ComponentsIndole-3-pyruvate decarboxylase
KeywordsLYASE / thiamine diphosphate / indole-3-acetic acid / indolepyruvate / tdp dependent enzyme / decarboxylase
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, Enterobacteriaceae / : / 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 ...Indole-3-pyruvate decarboxylase, Enterobacteriaceae / : / 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 / Indole-3-pyruvate decarboxylase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsSchutz, A. / Sandalova, T. / Ricagno, S. / Hubner, G. / Konig, S. / Schneider, G.
CitationJournal: Eur.J.Biochem. / Year: 2003
Title: Crystal structure of thiamindiphosphate-dependent indolepyruvate decarboxylase from Enterobacter cloacae, an enzyme involved in the biosynthesis of the plant hormone indole-3-acetic acid
Authors: Schutz, A. / Sandalova, T. / Ricagno, S. / Hubner, G. / Konig, S. / Schneider, G.
History
DepositionMar 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_conn.ptnr2_label_seq_id / _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: Indole-3-pyruvate decarboxylase
B: Indole-3-pyruvate decarboxylase
C: Indole-3-pyruvate decarboxylase
D: Indole-3-pyruvate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,14812
Polymers240,3494
Non-polymers1,7988
Water6,251347
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21970 Å2
ΔGint-179 kcal/mol
Surface area66800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.200, 151.620, 107.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Indole-3-pyruvate decarboxylase / Indolepyruvate decarboxylase


Mass: 60087.289 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: IPDC / Plasmid: pIP362 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P23234, indolepyruvate decarboxylase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 2.28 Å3/Da / Density % sol: 45.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEGmme, Na citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14 mg/mlenzyme1drop
220 mMMES/NaOH1droppH6.5
31 mMdithiothreitol1drop
40.1 Msodium citrate1reservoirpH5.0
58-12 %(w/v)PEG1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 11, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.65→29.56 Å / Num. all: 63376 / Num. obs: 63376 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 44.9 Å2 / Limit h max: 49 / Limit h min: 0 / Limit k max: 57 / Limit k min: 0 / Limit l max: 40 / Limit l min: 0 / Observed criterion F max: 2754137.27 / Observed criterion F min: 25.6 / Rsym value: 0.087 / Net I/σ(I): 7.8
Reflection shellResolution: 2.65→2.77 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.369 / % possible all: 99.9
Reflection
*PLUS
Num. obs: 63426 / Num. measured all: 315465 / Rmerge(I) obs: 0.087
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.369

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZPD

1zpd


Resolution: 2.65→29.56 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.236 3198 5 %RANDOM
Rwork0.205 ---
all0.207 63410 --
obs0.207 63376 99.9 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 22.125 Å2 / ksol: 0.33713 e/Å3
Displacement parametersBiso max: 93.33 Å2 / Biso mean: 33.42 Å2 / Biso min: 2.47 Å2
Baniso -1Baniso -2Baniso -3
1--5.8 Å20 Å20 Å2
2--5.13 Å20 Å2
3---0.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.36 Å
Luzzati d res high-2.65
Refinement stepCycle: LAST / Resolution: 2.65→29.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16404 0 108 347 16859
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_torsion_deg23.3
X-RAY DIFFRACTIONc_torsion_impr_deg0.88
LS refinement shellResolution: 2.65→2.77 Å / Rfactor Rfree error: 0.014
RfactorNum. reflection% reflection
Rfree0.28 409 5.2 %
Rwork0.292 7398 -
all-7827 -
obs-7807 99.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.388

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