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- PDB-1qlv: Pyrone synthase (PYS) from Gerbera hybrida -

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Basic information

Entry
Database: PDB / ID: 1qlv
TitlePyrone synthase (PYS) from Gerbera hybrida
ComponentsPYRONE SYNTHASE
KeywordsPOLYKETIDE SYNTHASE / POLYKETIDE / PYRONE BIOSYNTHESIS / CHALCONE
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / biosynthetic process / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Similarity search - Function
Chalcone/stilbene synthase, active site / Chalcone and stilbene synthases active site. / Chalcone/stilbene synthase, N-terminal / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Chalcone and stilbene synthases, N-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like ...Chalcone/stilbene synthase, active site / Chalcone and stilbene synthases active site. / Chalcone/stilbene synthase, N-terminal / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Chalcone and stilbene synthases, N-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesGERBERA HYBRIDA (plant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFerrer, J.-L. / Jez, J.M. / Bowman, M.E. / Schroder, J. / Noel, J.P.
CitationJournal: To be Published
Title: Pyrone Synthase (Pys) from Gerbera Hybrida
Authors: Ferrer, J.-L. / Jez, J.M. / Bowman, M.E. / Schroder, J. / Noel, J.P.
History
DepositionSep 16, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PYRONE SYNTHASE
B: PYRONE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)87,6672
Polymers87,6672
Non-polymers00
Water13,962775
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-10.9 kcal/mol
Surface area31160 Å2
MethodPQS
Unit cell
Length a, b, c (Å)82.140, 82.140, 241.325
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2017-

HOH

21B-2022-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.40676, 0.91352, -0.00397), (0.91349, 0.40678, 0.0082), (0.0091, -0.00029, -0.99996)
Vector: -2.27242, 1.13361, 120.35256)
DetailsBIOLOGICAL_UNIT: DIMERIC

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Components

#1: Protein PYRONE SYNTHASE / CHALCONE SYNTHASE 2 / NARINGENIN-CHALCONE SYNTHASE 2


Mass: 43833.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GERBERA HYBRIDA (plant) / Tissue: COROLLA / Plasmid: PHIS8 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P48391, chalcone synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 775 / 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: 2.12 Å3/Da / Density % sol: 42.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: HANGING DROP AT 4C, 1:1 25 MG/ML PYS + XTAL CONDITION (1.5 M AMMONIUM SULFATE, 0.05 M SUCCINIC ACID, PH 5.5, 2 MM DTT)

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: MAC SCIENCE MULTI WAVELENGTH SRA / Wavelength: 1.5418
DetectorType: BRUKER NONIUS DIP 2030 IMAGE PLATE / Detector: IMAGE PLATE / Date: Jul 15, 1999 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→41.07 Å / Num. obs: 48438 / % possible obs: 92.2 % / Redundancy: 16.5 % / Rsym value: 0.08 / Net I/σ(I): 16

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MODELISATION BASED ON PDB ENTRY 1BI5

1bi5


Resolution: 2.1→10 Å / Num. parameters: 26723 / Num. restraintsaints: 24588 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: THE C-TERMINAL RESIDUE WAS NOT SEEN IN THE DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.2689 2572 5 %RANDOM
all0.185 48438 --
obs0.1808 -87.5 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 14 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 6561.94
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5780 0 0 775 6555
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.023
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0251
X-RAY DIFFRACTIONs_zero_chiral_vol0.029
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.042
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.023
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.083
X-RAY DIFFRACTIONs_approx_iso_adps0

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