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- PDB-5er8: Crystal structure of cyclization domain of Phomopsis amygdali fus... -

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Basic information

Entry
Database: PDB / ID: 5er8
TitleCrystal structure of cyclization domain of Phomopsis amygdali fusicoccadiene synthase complexed with manganese ions and neridronate
ComponentsFusicoccadiene synthaseFusicocca-2,10(14)-diene synthase
KeywordsLYASE / diterpene cyclase / terpenoids
Function / homology
Function and homology information


fusicocca-2,10(14)-diene synthase / alcohol biosynthetic process / mycotoxin biosynthetic process / geranylgeranyl diphosphate synthase / farnesyltranstransferase activity / isoprenoid biosynthetic process / lyase activity / metal ion binding
Similarity search - Function
Terpene synthase family 2, C-terminal metal binding / Polyprenyl synthases signature 1. / Polyprenyl synthases signature 2. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Chem-NRD / Fusicoccadiene synthase
Similarity search - Component
Biological speciesPhomopsis amygdali (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsChen, M. / Christianson, D.W.
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: Structure and Function of Fusicoccadiene Synthase, a Hexameric Bifunctional Diterpene Synthase.
Authors: Chen, M. / Chou, W.K. / Toyomasu, T. / Cane, D.E. / Christianson, D.W.
History
DepositionNov 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fusicoccadiene synthase
B: Fusicoccadiene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,50615
Polymers83,3872
Non-polymers1,12013
Water1,36976
1
A: Fusicoccadiene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2267
Polymers41,6931
Non-polymers5326
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fusicoccadiene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2818
Polymers41,6931
Non-polymers5877
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)142.601, 142.601, 117.632
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Fusicoccadiene synthase / Fusicocca-2,10(14)-diene synthase / FS / PaDC4:GGS / Diterpene cyclase 4 / DC 4


Mass: 41693.266 Da / Num. of mol.: 2 / Fragment: Fusicocca-2,10(14)-diene synthase, residues 1-344
Source method: isolated from a genetically manipulated source
Details: Neridronate / Source: (gene. exp.) Phomopsis amygdali (fungus) / Gene: PaFS / Production host: Escherichia coli (E. coli)
References: UniProt: A2PZA5, fusicocca-2,10(14)-diene synthase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-NRD / (6-azanyl-1-oxidanyl-1-phosphono-hexyl)phosphonic acid / Neridronic acid


Mass: 277.149 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H17NO7P2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.14 Å3/Da / Density % sol: 70.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 1.05 M sodium formate, 0.075 M manganese formate, 0.1 M sodium acetate (pH 4.4)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.18 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18 Å / Relative weight: 1
ReflectionResolution: 2.5→43.4 Å / Num. obs: 48128 / % possible obs: 100 % / Redundancy: 8.4 % / Net I/σ(I): 30

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Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→43.386 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.26 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2385 2383 4.95 %
Rwork0.2068 --
obs0.2245 48098 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→43.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4853 0 43 76 4972
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115000
X-RAY DIFFRACTIONf_angle_d1.266775
X-RAY DIFFRACTIONf_dihedral_angle_d16.6841834
X-RAY DIFFRACTIONf_chiral_restr0.057728
X-RAY DIFFRACTIONf_plane_restr0.008856
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5009-2.55180.34271540.31852603X-RAY DIFFRACTION94
2.5518-2.60720.28441180.31752665X-RAY DIFFRACTION96
2.6072-2.66780.43651260.34052666X-RAY DIFFRACTION95
2.6678-2.73440.39571340.33562661X-RAY DIFFRACTION95
2.7344-2.80820.32311350.30442661X-RAY DIFFRACTION95
2.8082-2.89060.31671550.29552638X-RAY DIFFRACTION94
2.8906-2.98370.31381200.30252669X-RAY DIFFRACTION96
2.9837-3.09010.32351480.29812677X-RAY DIFFRACTION95
3.0901-3.21340.32311450.28172653X-RAY DIFFRACTION95
3.2134-3.35920.28341490.27162650X-RAY DIFFRACTION95
3.3592-3.53560.28871560.26072651X-RAY DIFFRACTION94
3.5356-3.7560.27441480.24772690X-RAY DIFFRACTION95
3.756-4.04430.25151540.21962661X-RAY DIFFRACTION95
4.0443-4.44820.22191420.18752693X-RAY DIFFRACTION95
4.4482-5.08470.2361250.18112728X-RAY DIFFRACTION96
5.0847-6.37950.19911470.18482731X-RAY DIFFRACTION95
6.3795-21.79730.21421270.1732840X-RAY DIFFRACTION96

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