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- PDB-1mvl: PPC decarboxylase mutant C175S -

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Basic information

Entry
Database: PDB / ID: 1mvl
TitlePPC decarboxylase mutant C175S
ComponentsPPC decarboxylase AtHAL3a
KeywordsLYASE / Flavoprotein / PPC decarboxylase / active site mutant C175S
Function / homology
Function and homology information


phosphopantothenoylcysteine decarboxylase / phosphopantothenoylcysteine decarboxylase activity / hyperosmotic salinity response / coenzyme A biosynthetic process
Similarity search - Function
Flavin prenyltransferase-like / Flavoprotein / Flavin prenyltransferase-like / Flavoprotein / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Phosphopantothenoylcysteine decarboxylase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsSteinbacher, S. / Hernandez-Acosta, P. / Bieseler, B. / Blaesse, M. / Huber, R. / Culianez-Macia, F.A. / Kupke, T.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Crystal Structure of the Plant PPC Decarboxylase AtHAL3a Complexed with an Ene-thiol Reaction Intermediate
Authors: Steinbacher, S. / Hernandez-Acosta, P. / Bieseler, B. / Blaesse, M. / Huber, R. / Culianez-Macia, F.A. / Kupke, T.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: Arabidopsis thaliana flavoprotein AtHAL3a catalyzes the decarboxylation of 4'-phosphopantothenoylcysteine to 4'-phosphopantetheine, a key step in coenzyme A biosynthesis
Authors: Kupke, T. / Hernandez-Acosta, P. / Steinbacher, S. / Culianez-Macia, F.A.
#2: Journal: J.Biol.Chem. / Year: 2002
Title: Molecular characterization of the Arabidopsis thaliana flavoprotein AtHAL3a reveals the general reaction mechanism of 4'-phosphopantothenoylcysteine decarboxylases
Authors: Hernandez-Acosta, P. / Schmid, D.G. / Jung, G. / Culianez-Macia, F.A. / Kupke, T.
#3: Journal: Plant J. / Year: 1999
Title: Arabidopsis thaliana AtHal3: a flavoprotein related to salt and osmotic tolerance and plant growth
Authors: Espinosa-Ruiz, A. / Belles, J.M. / Serrano, R. / Culianez-Macia, F.A.
#4: Journal: Structure / Year: 2000
Title: The X-ray structure of the FMN-binding protein AtHal3 provides the structural basis for the activity of a regulatory subunit involved in signal transduction
Authors: Albert, A. / Martinez-Ripoll, M. / Espinosa-Ruiz, A. / Yenush, L. / Culianez-Macia, F.A. / Serrano, R.
History
DepositionSep 26, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PPC decarboxylase AtHAL3a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8212
Polymers23,3651
Non-polymers4561
Water3,153175
1
A: PPC decarboxylase AtHAL3a
hetero molecules

A: PPC decarboxylase AtHAL3a
hetero molecules

A: PPC decarboxylase AtHAL3a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4636
Polymers70,0943
Non-polymers1,3693
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
MethodPQS
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.790, 111.790, 32.996
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit by the three-fold axis

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Components

#1: Protein PPC decarboxylase AtHAL3a / Halotolerance protein Hal3a


Mass: 23364.775 Da / Num. of mol.: 1 / Mutation: C175S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli)
References: UniProt: Q9SWE5, phosphopantothenoylcysteine decarboxylase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.71 Å3/Da / Density % sol: 54.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: ammonium sulphate, imidazole, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
220 mMTris-HCl1droppH7.5
31.4 Mammonium sulfate1reservoir
4100 mMimidazole-HCl1reservoirpH6.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 26, 2002 / Details: mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 15995 / Num. obs: 15995 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.06
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.22 / % possible all: 98.4
Reflection
*PLUS
Lowest resolution: 20 Å / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 98.4 % / Rmerge(I) obs: 0.22

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1E20

1e20


Resolution: 2→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2025 781 -random
Rwork0.1693 ---
all0.1702 15987 --
obs0.1702 15987 98.2 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.106 Å20.405 Å20 Å2
2--5.106 Å20 Å2
3----10.211 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1364 0 31 175 1570
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.53
X-RAY DIFFRACTIONc_mcbond_it2.4371.5
X-RAY DIFFRACTIONc_mcangle_it3.1132
X-RAY DIFFRACTIONc_scbond_it3.4822
X-RAY DIFFRACTIONc_scangle_it4.6582.5
LS refinement shellResolution: 2→20 Å
RfactorNum. reflection
Rfree0.2025 781
Rwork0.1693 -
obs-15987
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5fmn.param
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.203 / Rfactor Rwork: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS

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