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- PDB-1z1e: Crystal structure of stilbene synthase from Arachis hypogaea -

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Basic information

Entry
Database: PDB / ID: 1z1e
TitleCrystal structure of stilbene synthase from Arachis hypogaea
Componentsstilbene synthase
KeywordsTRANSFERASE / stilbene / type III polyketide synthase / STS
Function / homology
Function and homology information


polyketide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl 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
CITRIC ACID / Resveratrol synthase
Similarity search - Component
Biological speciesArachis hypogaea (peanut)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsShomura, Y. / Torayama, I. / Suh, D.Y. / Xiang, T. / Kita, A. / Sankawa, U. / Miki, K.
CitationJournal: Proteins / Year: 2005
Title: Crystal structure of stilbene synthase from Arachis hypogaea
Authors: Shomura, Y. / Torayama, I. / Suh, D.Y. / Xiang, T. / Kita, A. / Sankawa, U. / Miki, K.
History
DepositionMar 3, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 30, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: stilbene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2683
Polymers42,8831
Non-polymers3842
Water3,243180
1
A: stilbene synthase
hetero molecules

A: stilbene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5356
Polymers85,7672
Non-polymers7684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area6970 Å2
ΔGint-14 kcal/mol
Surface area27040 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)100.751, 100.751, 74.048
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-632-

HOH

21A-670-

HOH

DetailsThe second part of the biological assembly is generated by the two fold axis: y, x, -z

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Components

#1: Protein stilbene synthase


Mass: 42883.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arachis hypogaea (peanut) / Plasmid: pET32a, pET-STS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: Q9SLV5, trihydroxystilbene synthase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.58 Å3/Da / Density % sol: 51.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 100mM sodium citrate pH 4.6, 150mM ammonium sulfate, 16%(w/v) polyethylene glycol 6000, 10%(v/v) glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 19, 2001 / Details: Mirrors
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→57 Å / Num. all: 17189 / Num. obs: 17189 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 25.3 Å2 / Rsym value: 0.071 / Net I/σ(I): 14.7
Reflection shellResolution: 2.4→2.55 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.246 / % possible all: 95.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→37.59 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1455220.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.243 870 5.1 %RANDOM
Rwork0.206 ---
obs0.206 17171 99.2 %-
all-17189 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.4373 Å2 / ksol: 0.336106 e/Å3
Displacement parametersBiso mean: 28.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.32 Å21.73 Å20 Å2
2--1.32 Å20 Å2
3----2.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.4→37.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2982 0 26 180 3188
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d1.32
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it1.992
X-RAY DIFFRACTIONc_scbond_it2.092
X-RAY DIFFRACTIONc_scangle_it3.012.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.291 144 5.3 %
Rwork0.26 2576 -
obs--96 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION3CIT.PARCIT.TOP
X-RAY DIFFRACTION4WATER.PARAMWATER.TOP

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