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- PDB-1xet: Crystal structure of stilbene synthase from Pinus sylvestris, com... -

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Basic information

Entry
Database: PDB / ID: 1xet
TitleCrystal structure of stilbene synthase from Pinus sylvestris, complexed with methylmalonyl CoA
ComponentsDihydropinosylvin synthase
KeywordsTRANSFERASE
Function / homology
Function and homology information


pinosylvin synthase / pinosylvin synthase activity / polyketide biosynthetic process / cytoplasm
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
3-(1H-INDOL-3-YL)-2-OXOPROPANOIC ACID / METHYLMALONYL-COENZYME A / Pinosylvin synthase
Similarity search - Component
Biological speciesPinus sylvestris (Scots pine)
MethodX-RAY DIFFRACTION / isomorphous replacement / Resolution: 2 Å
AuthorsNg, S.H. / Chirgadze, D. / Spiteller, D. / Li, T.L. / Spencer, J.B. / Blundell, T.L.
CitationJournal: To be Published
Title: Crystal structure of stilbene synthase from Pinus sylvestris, complexed with methylmalonyl CoA
Authors: Ng, S.H. / Chirgadze, D. / Spiteller, D. / Li, T.L. / Spencer, J.B. / Blundell, T.L.
History
DepositionSep 12, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Advisory / Data collection / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name / _software.version
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydropinosylvin synthase
B: Dihydropinosylvin synthase
C: Dihydropinosylvin synthase
D: Dihydropinosylvin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,2958
Polymers179,8174
Non-polymers1,4774
Water15,385854
1
A: Dihydropinosylvin synthase
B: Dihydropinosylvin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1123
Polymers89,9092
Non-polymers2031
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-25 kcal/mol
Surface area26030 Å2
MethodPISA
2
C: Dihydropinosylvin synthase
D: Dihydropinosylvin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,1835
Polymers89,9092
Non-polymers1,2743
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7920 Å2
ΔGint-44 kcal/mol
Surface area25720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.465, 111.190, 132.015
Angle α, β, γ (deg.)90.00, 93.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Dihydropinosylvin synthase / Stilbene synthase / STS / Pinosylvin-forming stilbene synthase


Mass: 44954.344 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pinus sylvestris (Scots pine) / Plasmid: pET28(a) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q02323, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-3IO / 3-(1H-INDOL-3-YL)-2-OXOPROPANOIC ACID


Mass: 203.194 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H9NO3
#3: Chemical ChemComp-MCA / METHYLMALONYL-COENZYME A


Mass: 867.607 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H40N7O19P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 854 / 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: 2.22 Å3/Da / Density % sol: 44.56 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 3.8
Details: PEG 4000, citric acid, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→22.58 Å / Num. obs: 96601 / Biso Wilson estimate: 17.7 Å2

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: isomorphous replacement / Resolution: 2→22.58 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / Rfactor Rfree error: 0.003 / SU B: 4.058 / SU ML: 0.112 / Data cutoff high absF: 2308085 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.201 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.223 4833 5 %RANDOM
Rwork0.195 ---
obs0.195 97245 91.9 %-
all-105899 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.8097 Å2 / ksol: 0.352407 e/Å3
Displacement parametersBiso mean: 27.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å2-0.16 Å2
2--1.74 Å20 Å2
3----0.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2→22.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11561 0 93 854 12508
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.256 818 4.8 %
Rwork0.227 16310 -
obs--97.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3cis_peptide.param
X-RAY DIFFRACTION4lig.par

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